http://edamontology.org/format_3820 |
|
http://www.geneontology.org/formats/oboInOwl#inSubset
|
http://purl.obolibrary.org/obo/edam#formats |
| http://purl.obolibrary.org/obo/edam#edam
|
|
http://www.w3.org/2000/01/rdf-schema#label
|
Relaxed PHYLIP Sequential
|
|
http://edamontology.org/created_in
|
1.20
|
|
http://edamontology.org/documentation
|
http://biopython.org/DIST/docs/api/Bio.AlignIO.PhylipIO-module.html |
| http://www.phylo.org/index.php/help/relaxed_phylip
|
|
http://www.geneontology.org/formats/oboInOwl#hasDefinition
|
Phylip multiple alignment sequence format, less stringent than PHYLIP sequential format (format_1998).
|
|
http://www.w3.org/1999/02/22-rdf-syntax-ns#type
|
http://www.w3.org/2002/07/owl#Class
|
|
http://www.geneontology.org/formats/oboInOwl#hasExactSynonym
|
Relaxed PHYLIP sequential format |
| Relaxed PHYLIP non-interleaved |
| Relaxed PHYLIP non-interleaved format
|
|
http://www.w3.org/2000/01/rdf-schema#comment
|
It differs from Phylip sequential format (format_1997) on length of the ID sequence. There no length restrictions on the ID, but whitespaces aren't allowed in the sequence ID/Name because one space separates the longest ID and the beginning of the sequence. Sequences IDs must be padded to the longest ID length.
|
|
http://www.w3.org/2000/01/rdf-schema#subClassOf
|
http://edamontology.org/format_2924
|
http://edamontology.org/data_3138 |
|
http://www.geneontology.org/formats/oboInOwl#inSubset
|
http://purl.obolibrary.org/obo/edam#obsolete
|
|
http://www.w3.org/2002/07/owl#deprecated
|
true
|
|
http://www.w3.org/2000/01/rdf-schema#label
|
Transcriptional features (report)
|
|
http://edamontology.org/created_in
|
beta13
|
|
http://www.geneontology.org/formats/oboInOwl#hasDefinition
|
Features concerning transcription of DNA into RNA including the regulation of transcription.
|
|
http://www.geneontology.org/formats/oboInOwl#consider
|
http://edamontology.org/data_3134
|
|
http://www.w3.org/1999/02/22-rdf-syntax-ns#type
|
http://www.w3.org/2002/07/owl#Class
|
|
http://www.w3.org/2000/01/rdf-schema#comment
|
This includes promoters, CAAT signals, TATA signals, -35 signals, -10 signals, GC signals, primer binding sites for initiation of transcription or reverse transcription, enhancer, attenuator, terminators and ribosome binding sites.
|
|
http://www.w3.org/2000/01/rdf-schema#subClassOf
|
http://www.w3.org/2002/07/owl#DeprecatedClass
|
|
http://edamontology.org/obsolete_since
|
1.5
|
http://edamontology.org/format_3819 |
|
http://www.geneontology.org/formats/oboInOwl#inSubset
|
http://purl.obolibrary.org/obo/edam#formats |
| http://purl.obolibrary.org/obo/edam#edam
|
|
http://www.w3.org/2000/01/rdf-schema#label
|
Relaxed PHYLIP Interleaved
|
|
http://edamontology.org/created_in
|
1.20
|
|
http://edamontology.org/documentation
|
http://biopython.org/DIST/docs/api/Bio.AlignIO.PhylipIO-module.html |
| http://www.phylo.org/index.php/help/relaxed_phylip
|
|
http://www.geneontology.org/formats/oboInOwl#hasDefinition
|
Phylip multiple alignment sequence format, less stringent than PHYLIP format.
|
|
http://www.w3.org/1999/02/22-rdf-syntax-ns#type
|
http://www.w3.org/2002/07/owl#Class
|
|
http://www.geneontology.org/formats/oboInOwl#hasExactSynonym
|
PHYLIP Interleaved format
|
|
http://www.w3.org/2000/01/rdf-schema#comment
|
It differs from Phylip Format (format_1997) on length of the ID sequence. There no length restrictions on the ID, but whitespaces aren't allowed in the sequence ID/Name because one space separates the longest ID and the beginning of the sequence. Sequences IDs must be padded to the longest ID length.
|
|
http://www.w3.org/2000/01/rdf-schema#subClassOf
|
http://edamontology.org/format_2924
|
http://edamontology.org/data_0905 |
|
http://www.geneontology.org/formats/oboInOwl#inSubset
|
http://purl.obolibrary.org/obo/edam#edam |
| http://purl.obolibrary.org/obo/edam#data
|
|
http://www.w3.org/2000/01/rdf-schema#label
|
Protein interaction raw data
|
|
http://edamontology.org/created_in
|
beta12orEarlier
|
|
http://www.geneontology.org/formats/oboInOwl#hasDefinition
|
Protein-protein interaction data from for example yeast two-hybrid analysis, protein microarrays, immunoaffinity chromatography followed by mass spectrometry, phage display etc.
|
|
http://www.w3.org/1999/02/22-rdf-syntax-ns#type
|
http://www.w3.org/2002/07/owl#Class
|
|
http://www.w3.org/2000/01/rdf-schema#comment
|
This is a broad data type and is used a placeholder for other, more specific types. It is primarily intended to help navigation of EDAM and would not typically be used for annotation.
|
|
http://www.w3.org/2000/01/rdf-schema#subClassOf
|
http://edamontology.org/data_3108
|
http://edamontology.org/operation_3087 |
|
http://www.geneontology.org/formats/oboInOwl#inSubset
|
http://purl.obolibrary.org/obo/edam#obsolete
|
|
http://www.w3.org/2002/07/owl#deprecated
|
true
|
|
http://www.w3.org/2000/01/rdf-schema#label
|
Protein sequence feature detection
|
|
http://edamontology.org/created_in
|
beta13
|
|
http://edamontology.org/deprecation_comment
|
(jison)This is a distinction made on basis of input; all features exist can be mapped to a sequence so this isn't needed (consolidate with "Protein feature detection").
|
|
http://www.geneontology.org/formats/oboInOwl#hasDefinition
|
Predict, recognise and identify functional or other key sites within protein sequences, typically by scanning for known motifs, patterns and regular expressions.
|
|
http://www.w3.org/1999/02/22-rdf-syntax-ns#type
|
http://www.w3.org/2002/07/owl#Class
|
|
http://www.geneontology.org/formats/oboInOwl#replacedBy
|
http://edamontology.org/operation_3092
|
|
http://edamontology.org/oldParent
|
http://edamontology.org/operation_0253 |
| http://edamontology.org/operation_2479 |
| http://edamontology.org/operation_3092
|
|
http://www.w3.org/2000/01/rdf-schema#subClassOf
|
http://www.w3.org/2002/07/owl#DeprecatedClass
|
|
http://edamontology.org/obsolete_since
|
1.17
|
http://edamontology.org/format_3887 |
|
http://www.geneontology.org/formats/oboInOwl#inSubset
|
http://purl.obolibrary.org/obo/edam#formats |
| http://purl.obolibrary.org/obo/edam#edam
|
|
http://www.w3.org/2000/01/rdf-schema#label
|
CHARMM rtf
|
|
http://edamontology.org/created_in
|
1.22
|
|
http://www.geneontology.org/formats/oboInOwl#hasDefinition
|
Format of CHARMM Residue Topology Files (RTF), which define groups by including the atoms, the properties of the group, and bond and charge information.
|
|
http://www.w3.org/1999/02/22-rdf-syntax-ns#type
|
http://www.w3.org/2002/07/owl#Class
|
|
http://www.w3.org/2000/01/rdf-schema#comment
|
There is currently no tool available for conversion between GROMACS topology format and other formats, due to the internal differences in both approaches. There is, however, a method to convert small molecules parameterized with AMBER force-field into GROMACS format, allowing simulations of these systems with GROMACS MD package.
|
|
http://www.w3.org/2000/01/rdf-schema#subClassOf
|
http://edamontology.org/format_3879 |
| http://edamontology.org/format_2330 |
| http://edamontology.org/format_2033
|
http://edamontology.org/format_3883 |
|
http://www.geneontology.org/formats/oboInOwl#inSubset
|
http://purl.obolibrary.org/obo/edam#formats |
| http://purl.obolibrary.org/obo/edam#edam
|
|
http://www.w3.org/2000/01/rdf-schema#label
|
GROMACS itp
|
|
http://edamontology.org/created_in
|
1.22
|
|
http://www.geneontology.org/formats/oboInOwl#hasDefinition
|
GROMACS itp files (include topology) contain structure topology information, and are tipically included in GROMACS topology files (GROMACS top). Itp files are used to define individual (or multiple) components of a topology as a separate file. This is particularly useful if there is a molecule that is used frequently, and also reduces the size of the system topology file, splitting it in different parts.
|
|
http://edamontology.org/documentation
|
http://manual.gromacs.org/documentation/2018/user-guide/file-formats.html#itp
|
|
http://www.w3.org/1999/02/22-rdf-syntax-ns#type
|
http://www.w3.org/2002/07/owl#Class
|
|
http://www.w3.org/2000/01/rdf-schema#comment
|
GROMACS itp files are used also to define position restrictions on the molecule, or to define the force field parameters for a particular ligand.
|
|
http://www.w3.org/2000/01/rdf-schema#subClassOf
|
http://edamontology.org/format_3879 |
| http://edamontology.org/format_3884 |
| http://edamontology.org/format_2330 |
| http://edamontology.org/format_2033
|
http://edamontology.org/format_3885 |
|
http://www.geneontology.org/formats/oboInOwl#inSubset
|
http://purl.obolibrary.org/obo/edam#formats |
| http://purl.obolibrary.org/obo/edam#edam
|
|
http://www.w3.org/2000/01/rdf-schema#label
|
BinPos
|
|
http://edamontology.org/created_in
|
1.22
|
|
http://www.geneontology.org/formats/oboInOwl#hasDefinition
|
Scripps Research Institute BinPos format is a binary formatted file to store atom coordinates.
|
|
http://www.w3.org/1999/02/22-rdf-syntax-ns#type
|
http://www.w3.org/2002/07/owl#Class
|
|
http://www.geneontology.org/formats/oboInOwl#hasExactSynonym
|
Scripps Research Institute BinPos
|
|
http://www.w3.org/2000/01/rdf-schema#comment
|
It is basically a translation of the ASCII atom coordinate format to binary code. The only additional information stored is a magic number that identifies the BinPos format and the number of atoms per snapshot. The remainder is the chain of coordinates binary encoded. A drawback of this format is its architecture dependency. Integers and floats codification depends on the architecture, thus it needs to be converted if working in different platforms (little endian, big endian).
|
|
http://www.w3.org/2000/01/rdf-schema#subClassOf
|
http://edamontology.org/format_3867 |
| http://edamontology.org/format_2333
|
http://edamontology.org/data_1380 |
|
http://www.geneontology.org/formats/oboInOwl#inSubset
|
http://purl.obolibrary.org/obo/edam#obsolete
|
|
http://www.w3.org/2002/07/owl#deprecated
|
true
|
|
http://www.w3.org/2000/01/rdf-schema#label
|
Protein post-translational modification signature
|
|
http://edamontology.org/created_in
|
beta12orEarlier
|
|
http://www.geneontology.org/formats/oboInOwl#consider
|
http://edamontology.org/data_2071
|
|
http://www.geneontology.org/formats/oboInOwl#hasDefinition
|
A protein post-translational modification signature (sequence classifier) from the InterPro database.
|
|
http://www.w3.org/1999/02/22-rdf-syntax-ns#type
|
http://www.w3.org/2002/07/owl#Class
|
|
http://www.w3.org/2000/01/rdf-schema#comment
|
A protein post-translational modification signature corresponds to sites that undergo modification of the primary structure, typically to activate or de-activate a function. For example, methylation, sumoylation, glycosylation etc. The modification might be permanent or reversible.
|
|
http://www.w3.org/2000/01/rdf-schema#subClassOf
|
http://www.w3.org/2002/07/owl#DeprecatedClass
|
|
http://edamontology.org/obsolete_since
|
1.4
|
http://edamontology.org/data_1379 |
|
http://www.geneontology.org/formats/oboInOwl#inSubset
|
http://purl.obolibrary.org/obo/edam#obsolete
|
|
http://www.w3.org/2002/07/owl#deprecated
|
true
|
|
http://www.w3.org/2000/01/rdf-schema#label
|
Protein binding site signature
|
|
http://edamontology.org/created_in
|
beta12orEarlier
|
|
http://www.geneontology.org/formats/oboInOwl#hasDefinition
|
A protein binding site signature (sequence classifier) from the InterPro database.
|
|
http://www.geneontology.org/formats/oboInOwl#consider
|
http://edamontology.org/data_2071
|
|
http://www.w3.org/1999/02/22-rdf-syntax-ns#type
|
http://www.w3.org/2002/07/owl#Class
|
|
http://www.w3.org/2000/01/rdf-schema#comment
|
A protein binding site signature corresponds to a site that reversibly binds chemical compounds, which are not themselves substrates of the enzymatic reaction. This includes enzyme cofactors and residues involved in electron transport or protein structure modification.
|
|
http://www.w3.org/2000/01/rdf-schema#subClassOf
|
http://www.w3.org/2002/07/owl#DeprecatedClass
|
|
http://edamontology.org/obsolete_since
|
1.4
|
http://edamontology.org/data_1378 |
|
http://www.geneontology.org/formats/oboInOwl#inSubset
|
http://purl.obolibrary.org/obo/edam#obsolete
|
|
http://www.w3.org/2002/07/owl#deprecated
|
true
|
|
http://www.w3.org/2000/01/rdf-schema#label
|
Protein active site signature
|
|
http://edamontology.org/created_in
|
beta12orEarlier
|
|
http://www.geneontology.org/formats/oboInOwl#consider
|
http://edamontology.org/data_2071
|
|
http://www.geneontology.org/formats/oboInOwl#hasDefinition
|
A protein active site signature (sequence classifier) from the InterPro database.
|
|
http://www.w3.org/1999/02/22-rdf-syntax-ns#type
|
http://www.w3.org/2002/07/owl#Class
|
|
http://www.w3.org/2000/01/rdf-schema#comment
|
A protein active site signature corresponds to an enzyme catalytic pocket. An active site typically includes non-contiguous residues, therefore multiple signatures may be required to describe an active site. ; residues involved in enzymatic reactions for which mutational data is typically available.
|
|
http://www.w3.org/2000/01/rdf-schema#subClassOf
|
http://www.w3.org/2002/07/owl#DeprecatedClass
|
|
http://edamontology.org/obsolete_since
|
1.4
|
http://edamontology.org/format_2573 |
|
http://www.geneontology.org/formats/oboInOwl#inSubset
|
http://purl.obolibrary.org/obo/edam#formats |
| http://purl.obolibrary.org/obo/edam#edam
|
|
http://www.geneontology.org/formats/oboInOwl#hasDbXref
|
https://samtools.github.io/hts-specs/SAMv1.pdf
|
|
http://www.w3.org/2000/01/rdf-schema#label
|
SAM
|
|
http://edamontology.org/created_in
|
beta12orEarlier
|
|
http://www.geneontology.org/formats/oboInOwl#hasDefinition
|
Sequence Alignment/Map (SAM) format for alignment of nucleotide sequences (e.g. sequencing reads) to (a) reference sequence(s). May contain base-call and alignment qualities and other data.
|
|
http://edamontology.org/documentation
|
https://samtools.github.io/hts-specs/SAMv1.pdf
|
|
http://www.w3.org/1999/02/22-rdf-syntax-ns#type
|
http://www.w3.org/2002/07/owl#Class
|
|
http://www.w3.org/2000/01/rdf-schema#comment
|
The format supports short and long reads (up to 128Mbp) produced by different sequencing platforms and is used to hold mapped data within the GATK and across the Broad Institute, the Sanger Centre, and throughout the 1000 Genomes project.
|
|
http://www.w3.org/2000/01/rdf-schema#subClassOf
|
http://edamontology.org/format_2920 |
| http://edamontology.org/format_2057 |
| http://edamontology.org/format_2330
|
http://edamontology.org/format_3877 |
|
http://www.geneontology.org/formats/oboInOwl#inSubset
|
http://purl.obolibrary.org/obo/edam#formats |
| http://purl.obolibrary.org/obo/edam#edam
|
|
http://www.w3.org/2000/01/rdf-schema#label
|
XYZ
|
|
http://edamontology.org/created_in
|
1.22
|
|
http://www.geneontology.org/formats/oboInOwl#hasDefinition
|
The XYZ chemical file format is widely supported by many programs, although many slightly different XYZ file formats coexist (Tinker XYZ, UniChem XYZ, etc.). Basic information stored for each atom in the system are x, y and z coordinates and atom element/atomic number.
|
|
http://www.w3.org/1999/02/22-rdf-syntax-ns#type
|
http://www.w3.org/2002/07/owl#Class
|
|
http://www.w3.org/2000/01/rdf-schema#comment
|
XYZ files are structured in this way: First line contains the number of atoms in the file. Second line contains a title, comment, or filename. Remaining lines contain atom information. Each line starts with the element symbol, followed by x, y and z coordinates in angstroms separated by whitespace. Multiple molecules or frames can be contained within one file, so it supports trajectory storage. XYZ files can be directly represented by a molecular viewer, as they contain all the basic information needed to build the 3D model.
|
|
http://www.w3.org/2000/01/rdf-schema#subClassOf
|
http://edamontology.org/format_3868 |
| http://edamontology.org/format_2330 |
| http://edamontology.org/format_2033
|
http://edamontology.org/format_3876 |
|
http://www.geneontology.org/formats/oboInOwl#inSubset
|
http://purl.obolibrary.org/obo/edam#formats |
| http://purl.obolibrary.org/obo/edam#edam |
| TNG
|
|
http://www.w3.org/2000/01/rdf-schema#label
|
TNG
|
|
http://edamontology.org/created_in
|
1.22
|
|
http://www.geneontology.org/formats/oboInOwl#hasDefinition
|
Trajectory Next Generation (TNG) is a format for storage of molecular simulation data. It is designed and implemented by the GROMACS development group, and it is called to be the substitute of the XTC format.
|
|
http://www.w3.org/1999/02/22-rdf-syntax-ns#type
|
http://www.w3.org/2002/07/owl#Class
|
|
http://www.geneontology.org/formats/oboInOwl#hasExactSynonym
|
Trajectory Next Generation format
|
|
http://www.w3.org/2000/01/rdf-schema#comment
|
Fully architecture-independent format, regarding both endianness and the ability to mix single/double precision trajectories and I/O libraries. Self-sufficient, it should not require any other files for reading, and all the data should be contained in a single file for easy transport. Temporal compression of data, improving the compression rate of the previous XTC format. Possibility to store meta-data with information about the simulation. Direct access to a particular frame. Efficient parallel I/O.
|
|
http://www.w3.org/2000/01/rdf-schema#subClassOf
|
http://edamontology.org/format_3867 |
| http://edamontology.org/format_2333
|
http://edamontology.org/format_3875 |
|
http://www.geneontology.org/formats/oboInOwl#inSubset
|
http://purl.obolibrary.org/obo/edam#formats |
| http://purl.obolibrary.org/obo/edam#edam
|
|
http://www.w3.org/2000/01/rdf-schema#label
|
XTC
|
|
http://edamontology.org/created_in
|
1.22
|
|
http://www.geneontology.org/formats/oboInOwl#hasDefinition
|
Portable binary format for trajectories produced by GROMACS package.
|
|
http://www.w3.org/1999/02/22-rdf-syntax-ns#type
|
http://www.w3.org/2002/07/owl#Class
|
|
http://www.w3.org/2000/01/rdf-schema#comment
|
XTC uses the External Data Representation (xdr) routines for writing and reading data which were created for the Unix Network File System (NFS). XTC files use a reduced precision (lossy) algorithm which works multiplying the coordinates by a scaling factor (typically 1000), so converting them to pm (GROMACS standard distance unit is nm). This allows an integer rounding of the values. Several other tricks are performed, such as making use of atom proximity information: atoms close in sequence are usually close in space (e.g. water molecules). That makes XTC format the most efficient in terms of disk usage, in most cases reducing by a factor of 2 the size of any other binary trajectory format.
|
|
http://www.w3.org/2000/01/rdf-schema#subClassOf
|
http://edamontology.org/format_3867 |
| http://edamontology.org/format_2333
|
http://edamontology.org/format_3874 |
|
http://www.geneontology.org/formats/oboInOwl#inSubset
|
http://purl.obolibrary.org/obo/edam#formats |
| http://purl.obolibrary.org/obo/edam#edam
|
|
http://www.w3.org/2000/01/rdf-schema#label
|
PCAzip
|
|
http://edamontology.org/created_in
|
1.22
|
|
http://www.geneontology.org/formats/oboInOwl#hasDefinition
|
PCAZip format is a binary compressed file to store atom coordinates based on Essential Dynamics (ED) and Principal Component Analysis (PCA).
|
|
http://www.w3.org/1999/02/22-rdf-syntax-ns#type
|
http://www.w3.org/2002/07/owl#Class
|
|
http://www.w3.org/2000/01/rdf-schema#comment
|
The compression is made projecting the Cartesian snapshots collected along the trajectory into an orthogonal space defined by the most relevant eigenvectors obtained by diagonalization of the covariance matrix (PCA). In the compression/decompression process, part of the original information is lost, depending on the final number of eigenvectors chosen. However, with a reasonable choice of the set of eigenvectors the compression typically reduces the trajectory file to less than one tenth of their original size with very acceptable loss of information. Compression with PCAZip can only be applied to unsolvated structures.
|
|
http://www.w3.org/2000/01/rdf-schema#subClassOf
|
http://edamontology.org/format_3867 |
| http://edamontology.org/format_2333
|
http://edamontology.org/format_3880 |
|
http://www.geneontology.org/formats/oboInOwl#inSubset
|
http://purl.obolibrary.org/obo/edam#formats |
| http://purl.obolibrary.org/obo/edam#edam
|
|
http://www.w3.org/2000/01/rdf-schema#label
|
GROMACS top
|
|
http://edamontology.org/created_in
|
1.22
|
|
http://www.geneontology.org/formats/oboInOwl#hasDefinition
|
GROMACS MD package top textual files define an entire structure system topology, either directly, or by including itp files.
|
|
http://edamontology.org/documentation
|
http://manual.gromacs.org/documentation/2018/user-guide/file-formats.html#top
|
|
http://www.w3.org/1999/02/22-rdf-syntax-ns#type
|
http://www.w3.org/2002/07/owl#Class
|
|
http://www.w3.org/2000/01/rdf-schema#comment
|
There is currently no tool available for conversion between GROMACS topology format and other formats, due to the internal differences in both approaches. There is, however, a method to convert small molecules parameterized with AMBER force-field into GROMACS format, allowing simulations of these systems with GROMACS MD package.
|
|
http://www.w3.org/2000/01/rdf-schema#subClassOf
|
http://edamontology.org/format_3879 |
| http://edamontology.org/format_2330 |
| http://edamontology.org/format_2033
|
http://edamontology.org/format_3882 |
|
http://www.geneontology.org/formats/oboInOwl#inSubset
|
http://purl.obolibrary.org/obo/edam#formats |
| http://purl.obolibrary.org/obo/edam#edam
|
|
http://www.w3.org/2000/01/rdf-schema#label
|
PSF
|
|
http://edamontology.org/created_in
|
1.22
|
|
http://www.geneontology.org/formats/oboInOwl#hasDefinition
|
X-Plor Protein Structure Files (PSF) are structure topology files used by NAMD and CHARMM molecular simulations programs. PSF files contain six main sections of interest: atoms, bonds, angles, dihedrals, improper dihedrals (force terms used to maintain planarity) and cross-terms.
|
|
http://edamontology.org/documentation
|
http://www.ks.uiuc.edu/Training/TutorialsOverview/namd/namd-tutorial-unix-html/node23.html
|
|
http://www.w3.org/1999/02/22-rdf-syntax-ns#type
|
http://www.w3.org/2002/07/owl#Class
|
|
http://www.w3.org/2000/01/rdf-schema#comment
|
The high similarity in the functional form of the two potential energy functions used by AMBER and CHARMM force-fields gives rise to the possible use of one force-field within the other MD engine. Therefore, the conversion of PSF files to AMBER Prmtop format is possible with the use of AMBER chamber (CHARMM - AMBER) program.
|
|
http://www.w3.org/2000/01/rdf-schema#subClassOf
|
http://edamontology.org/format_3879 |
| http://edamontology.org/format_2330 |
| http://edamontology.org/format_2033
|
http://edamontology.org/format_3881 |
|
http://www.geneontology.org/formats/oboInOwl#inSubset
|
http://purl.obolibrary.org/obo/edam#formats |
| http://purl.obolibrary.org/obo/edam#edam
|
|
http://www.w3.org/2000/01/rdf-schema#label
|
AMBER top
|
|
http://edamontology.org/created_in
|
1.22
|
|
http://edamontology.org/documentation
|
http://ambermd.org/formats.html#topology
|
|
http://www.geneontology.org/formats/oboInOwl#hasDefinition
|
AMBER Prmtop file (version 7) is a structure topology text file divided in several sections designed to be parsed easily using simple Fortran code. Each section contains particular topology information, such as atom name, charge, mass, angles, dihedrals, etc.
|
|
http://www.w3.org/1999/02/22-rdf-syntax-ns#type
|
http://www.w3.org/2002/07/owl#Class
|
|
http://www.geneontology.org/formats/oboInOwl#hasExactSynonym
|
AMBER Parm7 |
| Prmtop7 |
| Parm7 |
| Prmtop |
| AMBER Parm
|
|
http://www.w3.org/2000/01/rdf-schema#comment
|
It can be modified manually, but as the size of the system increases, the hand-editing becomes increasingly complex. AMBER Parameter-Topology file format is used extensively by the AMBER software suite and is referred to as the Prmtop file for short. |
| version 7 is written to distinguish it from old versions of AMBER Prmtop. Similarly to HDF5, it is a completely different format, according to AMBER group: a drastic change to the file format occurred with the 2004 release of Amber 7 (http://ambermd.org/prmtop.pdf)
|
|
http://www.w3.org/2000/01/rdf-schema#subClassOf
|
http://edamontology.org/format_3879 |
| http://edamontology.org/format_2330 |
| http://edamontology.org/format_2033
|
http://edamontology.org/format_3008 |
|
http://www.geneontology.org/formats/oboInOwl#inSubset
|
http://purl.obolibrary.org/obo/edam#formats |
| http://purl.obolibrary.org/obo/edam#edam
|
|
http://www.geneontology.org/formats/oboInOwl#hasDbXref
|
http://genome.ucsc.edu/FAQ/FAQformat#format5
|
|
http://www.w3.org/2000/01/rdf-schema#label
|
MAF
|
|
http://edamontology.org/created_in
|
beta12orEarlier
|
|
http://www.geneontology.org/formats/oboInOwl#hasDefinition
|
Multiple Alignment Format (MAF) supporting alignments of whole genomes with rearrangements, directions, multiple pieces to the alignment, and so forth.
|
|
http://edamontology.org/documentation
|
http://genome.ucsc.edu/FAQ/FAQformat#format5
|
|
http://www.w3.org/1999/02/22-rdf-syntax-ns#type
|
http://www.w3.org/2002/07/owl#Class
|
|
http://www.w3.org/2000/01/rdf-schema#comment
|
Typically generated by Multiz and TBA aligners; can be displayed in a genome browser like a sequence annotation track. This should not be confused with MIRA Assembly Format or Mutation Annotation Format.
|
|
http://www.w3.org/2000/01/rdf-schema#subClassOf
|
http://edamontology.org/format_2554 |
| http://edamontology.org/format_2919 |
| http://edamontology.org/format_2330
|
http://edamontology.org/data_0852 |
|
http://www.geneontology.org/formats/oboInOwl#inSubset
|
http://purl.obolibrary.org/obo/edam#obsolete
|
|
http://www.w3.org/2002/07/owl#deprecated
|
true
|
|
http://www.w3.org/2000/01/rdf-schema#label
|
Sequence mask type
|
|
http://edamontology.org/created_in
|
beta12orEarlier
|
|
http://www.geneontology.org/formats/oboInOwl#hasDefinition
|
A label (text token) describing the type of sequence masking to perform.
|
|
http://www.geneontology.org/formats/oboInOwl#consider
|
http://edamontology.org/data_0842
|
|
http://www.w3.org/1999/02/22-rdf-syntax-ns#type
|
http://www.w3.org/2002/07/owl#Class
|
|
http://www.w3.org/2000/01/rdf-schema#comment
|
Sequence masking is where specific characters or positions in a molecular sequence are masked (replaced) with an another (mask character). The mask type indicates what is masked, for example regions that are not of interest or which are information-poor including acidic protein regions, basic protein regions, proline-rich regions, low compositional complexity regions, short-periodicity internal repeats, simple repeats and low complexity regions. Masked sequences are used in database search to eliminate statistically significant but biologically uninteresting hits.
|
|
http://www.w3.org/2000/01/rdf-schema#subClassOf
|
http://www.w3.org/2002/07/owl#DeprecatedClass
|
|
http://edamontology.org/obsolete_since
|
1.5
|
http://edamontology.org/data_3029 |
|
http://www.geneontology.org/formats/oboInOwl#inSubset
|
http://purl.obolibrary.org/obo/edam#edam |
| http://purl.obolibrary.org/obo/edam#data |
| http://purl.obolibrary.org/obo/edam#identifiers
|
|
http://www.w3.org/2000/01/rdf-schema#label
|
Protein ID (EMBL/GenBank/DDBJ)
|
|
http://edamontology.org/created_in
|
beta13
|
|
http://www.geneontology.org/formats/oboInOwl#hasDefinition
|
EMBL/GENBANK/DDBJ coding feature protein identifier, issued by International collaborators.
|
|
http://www.w3.org/1999/02/22-rdf-syntax-ns#type
|
http://www.w3.org/2002/07/owl#Class
|
|
http://www.w3.org/2000/01/rdf-schema#comment
|
This qualifier consists of a stable ID portion (3+5 format with 3 position letters and 5 numbers) plus a version number after the decimal point. When the protein sequence encoded by the CDS changes, only the version number of the /protein_id value is incremented; the stable part of the /protein_id remains unchanged and as a result will permanently be associated with a given protein; this qualifier is valid only on CDS features which translate into a valid protein.
|
|
http://www.w3.org/2000/01/rdf-schema#subClassOf
|
http://edamontology.org/data_2091 |
| http://edamontology.org/data_2907
|
http://edamontology.org/data_3031 |
|
http://www.geneontology.org/formats/oboInOwl#inSubset
|
http://purl.obolibrary.org/obo/edam#obsolete
|
|
http://www.w3.org/2002/07/owl#deprecated
|
true
|
|
http://www.w3.org/2000/01/rdf-schema#label
|
Core data
|
|
http://edamontology.org/created_in
|
beta13
|
|
http://www.geneontology.org/formats/oboInOwl#hasDefinition
|
A type of data that (typically) corresponds to entries from the primary biological databases and which is (typically) the primary input or output of a tool, i.e. the data the tool processes or generates, as distinct from metadata and identifiers which describe and identify such core data, parameters that control the behaviour of tools, reports of derivative data generated by tools and annotation.
|
|
http://www.w3.org/1999/02/22-rdf-syntax-ns#type
|
http://www.w3.org/2002/07/owl#Class
|
|
http://www.geneontology.org/formats/oboInOwl#replacedBy
|
http://edamontology.org/data_0006
|
|
http://www.w3.org/2000/01/rdf-schema#comment
|
Core data entities typically have a format and may be identified by an accession number.
|
|
http://www.w3.org/2000/01/rdf-schema#subClassOf
|
http://www.w3.org/2002/07/owl#DeprecatedClass
|
|
http://edamontology.org/obsolete_since
|
1.5
|
http://edamontology.org/format_3906 |
|
http://www.geneontology.org/formats/oboInOwl#inSubset
|
http://purl.obolibrary.org/obo/edam#formats |
| http://purl.obolibrary.org/obo/edam#edam
|
|
http://www.w3.org/2000/01/rdf-schema#label
|
NMReDATA
|
|
http://edamontology.org/created_in
|
1.22
|
|
http://www.w3.org/2000/01/rdf-schema#seeAlso
|
http://nmredata.org/
|
|
http://www.geneontology.org/formats/oboInOwl#hasDefinition
|
MReData is a text based data standard for processed NMR data. It is relying on SDF molecule data and allows to store assignments of NMR peaks to molecule features. The NMR-extracted data (or “NMReDATA”) includes: Chemical shift,scalar coupling, 2D correlation, assignment, etc.
|
|
http://www.w3.org/1999/02/22-rdf-syntax-ns#type
|
http://www.w3.org/2002/07/owl#Class
|
|
http://www.w3.org/2000/01/rdf-schema#comment
|
NMReData is a text based data standard for processed NMR data. It is relying on SDF molecule data and allows to store assignments of NMR peaks to molecule features. The NMR-extracted data (or “NMReDATA”) includes: Chemical shift,scalar coupling, 2D correlation, assignment, etc. Find more in the paper at D. Jeannerat, Magn. Reson. in Chem., 2017, 55, 7-14.
|
|
http://www.w3.org/2000/01/rdf-schema#subClassOf
|
http://edamontology.org/format_3824 |
| http://edamontology.org/format_2330
|
http://edamontology.org/topic_0782 |
|
http://www.geneontology.org/formats/oboInOwl#hasDbXref
|
VT 1.5.21 Mycology
|
|
http://www.w3.org/2000/01/rdf-schema#label
|
Fungi
|
|
http://edamontology.org/created_in
|
beta12orEarlier
|
|
http://www.geneontology.org/formats/oboInOwl#consider
|
http://edamontology.org/topic_0621
|
|
http://edamontology.org/oldParent
|
http://edamontology.org/topic_2818
|
|
http://www.geneontology.org/formats/oboInOwl#inSubset
|
http://purl.obolibrary.org/obo/edam#obsolete
|
|
http://www.w3.org/2002/07/owl#deprecated
|
true
|
|
http://www.geneontology.org/formats/oboInOwl#hasNarrowSynonym
|
Yeast
|
|
http://edamontology.org/deprecation_comment
|
(jison)Out of EDAM scope. While very useful to have a basic set of IDs for organisms, should find a better way to provide this e.g. in bio.tools (NCBI taxon ID subset).
|
|
http://www.geneontology.org/formats/oboInOwl#hasDefinition
|
Fungi and molds, e.g. information on a specific fungal genome including molecular sequences, genes and annotation.
|
|
http://www.w3.org/1999/02/22-rdf-syntax-ns#type
|
http://www.w3.org/2002/07/owl#Class
|
|
http://www.w3.org/2000/01/rdf-schema#comment
|
The resource may be specific to a fungus, a group of fungi or all fungi.
|
|
http://www.w3.org/2000/01/rdf-schema#subClassOf
|
http://www.w3.org/2002/07/owl#DeprecatedClass
|
|
http://edamontology.org/obsolete_since
|
1.17
|
http://edamontology.org/topic_0783 |
|
http://www.geneontology.org/formats/oboInOwl#inSubset
|
http://purl.obolibrary.org/obo/edam#obsolete
|
|
http://www.w3.org/2002/07/owl#deprecated
|
true
|
|
http://www.w3.org/2000/01/rdf-schema#label
|
Pathogens
|
|
http://edamontology.org/created_in
|
beta12orEarlier
|
|
http://edamontology.org/deprecation_comment
|
(jison)Out of EDAM scope. While very useful to have a basic set of IDs for organisms, should find a better way to provide this e.g. in bio.tools (NCBI taxon ID subset). Definition is wrong anyway.
|
|
http://www.geneontology.org/formats/oboInOwl#hasDefinition
|
Pathogens, e.g. information on a specific vertebrate genome including molecular sequences, genes and annotation.
|
|
http://www.geneontology.org/formats/oboInOwl#consider
|
http://edamontology.org/topic_0621
|
|
http://www.w3.org/1999/02/22-rdf-syntax-ns#type
|
http://www.w3.org/2002/07/owl#Class
|
|
http://www.w3.org/2000/01/rdf-schema#comment
|
The resource may be specific to a pathogen, a group of pathogens or all pathogens.
|
|
http://edamontology.org/oldParent
|
http://edamontology.org/topic_0621
|
|
http://www.w3.org/2000/01/rdf-schema#subClassOf
|
http://www.w3.org/2002/07/owl#DeprecatedClass
|
|
http://edamontology.org/obsolete_since
|
1.17
|
http://edamontology.org/operation_3186 |
|
http://www.geneontology.org/formats/oboInOwl#inSubset
|
http://purl.obolibrary.org/obo/edam#edam |
| http://purl.obolibrary.org/obo/edam#operations
|
|
http://www.w3.org/2000/01/rdf-schema#label
|
Bisulfite mapping
|
|
http://edamontology.org/created_in
|
1.1
|
|
http://www.geneontology.org/formats/oboInOwl#hasDefinition
|
The mapping of methylation sites in a DNA (genome) sequence.
|
|
http://www.w3.org/1999/02/22-rdf-syntax-ns#type
|
http://www.w3.org/2002/07/owl#Class
|
|
http://www.geneontology.org/formats/oboInOwl#hasExactSynonym
|
Bisulfite sequence mapping |
| Bisulfite sequence alignment
|
|
http://www.w3.org/2000/01/rdf-schema#comment
|
Bisulfite mapping follows high-throughput sequencing of DNA which has undergone bisulfite treatment followed by PCR amplification; unmethylated cytosines are specifically converted to thymine, allowing the methylation status of cytosine in the DNA to be detected.
|
|
http://www.w3.org/2000/01/rdf-schema#subClassOf
|
http://edamontology.org/operation_3809 |
| http://edamontology.org/operation_2944
|
http://edamontology.org/format_1343 |
|
http://www.geneontology.org/formats/oboInOwl#inSubset
|
http://purl.obolibrary.org/obo/edam#formats |
| http://purl.obolibrary.org/obo/edam#edam
|
|
http://www.w3.org/2000/01/rdf-schema#label
|
InterPro match table format
|
|
http://edamontology.org/created_in
|
beta12orEarlier
|
|
http://www.geneontology.org/formats/oboInOwl#hasDefinition
|
Format of results of a search of the InterPro database showing matches between protein sequence(s) and signatures for an InterPro entry.
|
|
http://www.w3.org/1999/02/22-rdf-syntax-ns#type
|
http://www.w3.org/2002/07/owl#Class
|
|
http://www.w3.org/2000/01/rdf-schema#comment
|
The table presents matches between query proteins (rows) and signature methods (columns) for this entry. Alternatively the sequence(s) might be from from the InterPro entry itself. The match position in the protein sequence and match status (true positive, false positive etc) are indicated.
|
|
http://www.w3.org/2000/01/rdf-schema#subClassOf
|
http://edamontology.org/format_1341
|
http://edamontology.org/format_3164 |
|
http://www.geneontology.org/formats/oboInOwl#hasDbXref
|
https://hyperbrowser.uio.no/test/static/hyperbrowser/gtrack/GTrack_specification.txt |
| http://www.gtrack.no |
| https://hyperbrowser.uio.no/test/static/hyperbrowser/gtrack/GTrack_specification.html
|
|
http://www.w3.org/2000/01/rdf-schema#label
|
GTrack
|
|
http://edamontology.org/created_in
|
1.0
|
|
http://edamontology.org/example
|
https://hyperbrowser.uio.no/hb/u/hb-superuser/h/gtrack-examples-from-the-specification |
| https://github.com/gtrack/gtrack/tree/master/gtrack/examples
|
|
http://edamontology.org/documentation
|
https://hyperbrowser.uio.no/test/static/hyperbrowser/gtrack/GTrack_specification.txt |
| http://www.gtrack.no |
| https://hyperbrowser.uio.no/test/static/hyperbrowser/gtrack/GTrack_specification.html
|
|
http://www.geneontology.org/formats/oboInOwl#hasExactSynonym
|
BioXSD|GTrack GTrack |
| GTrack|BTrack|GSuite GTrack |
| GTrack|GSuite|BTrack GTrack |
| GTrack format |
| BioXSD/GTrack GTrack
|
|
http://www.geneontology.org/formats/oboInOwl#inSubset
|
http://purl.obolibrary.org/obo/edam#formats |
| http://purl.obolibrary.org/obo/edam#edam
|
|
http://www.geneontology.org/formats/oboInOwl#comment
|
'GTrack' belongs to the 'BioXSD|GTrack' ecosystem of generic formats, and particular to its subset, the 'GTrack ecosystem' (GTrack, GSuite, BTrack). 'GTrack' is the tabular format for representing features of sequences and genomes.
|
|
http://edamontology.org/citation
|
http://doi.org/10.1186/1471-2105-12-494
|
|
http://edamontology.org/repository
|
https://github.com/gtrack/gtrack
|
|
http://www.geneontology.org/formats/oboInOwl#hasDefinition
|
GTrack is a generic and optimised tabular format for genome or sequence feature tracks. GTrack unifies the power of other track formats (e.g. GFF3, BED, WIG), and while optimised in size, adds more flexibility, customisation, and automation ("machine understandability").
|
|
http://www.w3.org/1999/02/22-rdf-syntax-ns#type
|
http://www.w3.org/2002/07/owl#Class
|
|
http://www.w3.org/2000/01/rdf-schema#subClassOf
|
http://edamontology.org/format_2206 |
| http://edamontology.org/format_2919 |
| http://edamontology.org/format_2330
|
|
http://www.geneontology.org/formats/oboInOwl#hasBroadSynonym
|
GTrack ecosystem of formats
|
http://edamontology.org/data_1182 |
|
http://edamontology.org/regex
|
FMA:[0-9]+
|
|
http://www.geneontology.org/formats/oboInOwl#inSubset
|
http://purl.obolibrary.org/obo/edam#edam |
| http://purl.obolibrary.org/obo/edam#data |
| http://purl.obolibrary.org/obo/edam#identifiers
|
|
http://www.w3.org/2000/01/rdf-schema#label
|
FMA concept ID
|
|
http://edamontology.org/created_in
|
beta12orEarlier
|
|
http://www.geneontology.org/formats/oboInOwl#hasDefinition
|
An identifier of a concept from Foundational Model of Anatomy.
|
|
http://www.w3.org/1999/02/22-rdf-syntax-ns#type
|
http://www.w3.org/2002/07/owl#Class
|
|
http://www.w3.org/2000/01/rdf-schema#comment
|
Classifies anatomical entities according to their shared characteristics (genus) and distinguishing characteristics (differentia). Specifies the part-whole and spatial relationships of the entities, morphological transformation of the entities during prenatal development and the postnatal life cycle and principles, rules and definitions according to which classes and relationships in the other three components of FMA are represented.
|
|
http://www.w3.org/2000/01/rdf-schema#subClassOf
|
http://edamontology.org/data_2091 |
| http://edamontology.org/data_1087
|
http://edamontology.org/topic_3518 |
|
http://www.geneontology.org/formats/oboInOwl#inSubset
|
http://purl.obolibrary.org/obo/edam#topics |
| http://purl.obolibrary.org/obo/edam#edam
|
|
http://www.w3.org/2000/01/rdf-schema#label
|
Microarray experiment
|
|
http://edamontology.org/created_in
|
1.8
|
|
http://www.geneontology.org/formats/oboInOwl#hasNarrowSynonym
|
Tissue microarray |
| aCGH microarray |
| Genotyping array |
| Two channel microarray |
| Gene expression microarray |
| miRNA array |
| mRNA microarray |
| One channel microarray |
| Proprietary platform micoarray |
| Multichannel microarray |
| Reverse phase protein array |
| Methylation array |
| SNP array |
| MicroRNA array
|
|
http://www.w3.org/2000/01/rdf-schema#seeAlso
|
https://en.wikipedia.org/wiki/Microarray
|
|
http://www.geneontology.org/formats/oboInOwl#hasDefinition
|
Microarray experiments including conditions, protocol, sample:data relationships etc.
|
|
http://www.w3.org/1999/02/22-rdf-syntax-ns#type
|
http://www.w3.org/2002/07/owl#Class
|
|
http://www.geneontology.org/formats/oboInOwl#hasExactSynonym
|
Microarrays
|
|
http://www.w3.org/2000/01/rdf-schema#comment
|
This might specify which raw data file relates to which sample and information on hybridisations, e.g. which are technical and which are biological replicates.
|
|
http://www.geneontology.org/formats/oboInOwl#hasHumanReadableId
|
Microarray_experiment
|
|
http://www.w3.org/2000/01/rdf-schema#subClassOf
|
http://edamontology.org/topic_3361
|
http://edamontology.org/data_1164 |
|
http://www.geneontology.org/formats/oboInOwl#inSubset
|
http://purl.obolibrary.org/obo/edam#edam |
| http://purl.obolibrary.org/obo/edam#data |
| http://purl.obolibrary.org/obo/edam#identifiers
|
|
http://www.w3.org/2000/01/rdf-schema#label
|
MIRIAM URI
|
|
http://edamontology.org/created_in
|
beta12orEarlier
|
|
http://edamontology.org/example
|
urn:miriam:pubmed:16333295|urn:miriam:obo.go:GO%3A0045202
|
|
http://www.geneontology.org/formats/oboInOwl#hasDefinition
|
The URI (URL or URN) of a data entity from the MIRIAM database.
|
|
http://www.w3.org/1999/02/22-rdf-syntax-ns#type
|
http://www.w3.org/2002/07/owl#Class
|
|
http://www.geneontology.org/formats/oboInOwl#hasExactSynonym
|
identifiers.org synonym
|
|
http://www.w3.org/2000/01/rdf-schema#comment
|
A MIRIAM URI consists of the URI of the MIRIAM data type (PubMed, UniProt etc) followed by the identifier of an element of that data type, for example PMID for a publication or an accession number for a GO term.
|
|
http://www.w3.org/2000/01/rdf-schema#subClassOf
|
_:47 |
| http://edamontology.org/data_2902 |
| http://edamontology.org/data_2091 |
| http://edamontology.org/data_1047
|
http://edamontology.org/operation_0547 |
|
http://www.geneontology.org/formats/oboInOwl#inSubset
|
http://purl.obolibrary.org/obo/edam#edam |
| http://purl.obolibrary.org/obo/edam#operations
|
|
http://www.w3.org/2000/01/rdf-schema#label
|
Phylogenetic tree generation (maximum likelihood and Bayesian methods)
|
|
http://edamontology.org/created_in
|
beta12orEarlier
|
|
http://www.geneontology.org/formats/oboInOwl#hasDefinition
|
Construct a phylogenetic tree by relating sequence data to a hypothetical tree topology using a model of sequence evolution.
|
|
http://www.w3.org/1999/02/22-rdf-syntax-ns#type
|
http://www.w3.org/2002/07/owl#Class
|
|
http://www.geneontology.org/formats/oboInOwl#hasExactSynonym
|
Phylogenetic tree construction (maximum likelihood and Bayesian methods)
|
|
http://www.w3.org/2000/01/rdf-schema#comment
|
Maximum likelihood methods search for a tree that maximizes a likelihood function, i.e. that is most likely given the data and model. Bayesian analysis estimate the probability of tree for branch lengths and topology, typically using a Monte Carlo algorithm.
|
|
http://www.w3.org/2000/01/rdf-schema#subClassOf
|
http://edamontology.org/operation_0539
|
http://edamontology.org/operation_1841 |
|
http://www.geneontology.org/formats/oboInOwl#inSubset
|
http://purl.obolibrary.org/obo/edam#obsolete
|
|
http://www.geneontology.org/formats/oboInOwl#hasDbXref
|
WHATIF:ShowLikelyRotamers100 |
| WHATIF:ShowLikelyRotamers |
| WHATIF:ShowLikelyRotamers300 |
| WHATIF:ShowLikelyRotamers200 |
| WHATIF:ShowLikelyRotamers500 |
| WHATIF:ShowLikelyRotamers400 |
| WHATIF:ShowLikelyRotamers700 |
| WHATIF:ShowLikelyRotamers600 |
| WHATIF:ShowLikelyRotamers900 |
| WHATIF:ShowLikelyRotamers800
|
|
http://www.w3.org/2002/07/owl#deprecated
|
true
|
|
http://www.w3.org/2000/01/rdf-schema#label
|
Rotamer likelihood prediction
|
|
http://edamontology.org/created_in
|
beta12orEarlier
|
|
http://www.geneontology.org/formats/oboInOwl#hasDefinition
|
Predict rotamer likelihoods for all 20 amino acid types at each position in a protein structure.
|
|
http://www.w3.org/1999/02/22-rdf-syntax-ns#type
|
http://www.w3.org/2002/07/owl#Class
|
|
http://www.geneontology.org/formats/oboInOwl#replacedBy
|
http://edamontology.org/operation_0480
|
|
http://www.w3.org/2000/01/rdf-schema#comment
|
Output typically includes, for each residue position, the likelihoods for the 20 amino acid types with estimated reliability of the 20 likelihoods.
|
|
http://www.w3.org/2000/01/rdf-schema#subClassOf
|
http://www.w3.org/2002/07/owl#DeprecatedClass
|
|
http://edamontology.org/obsolete_since
|
1.12
|
http://edamontology.org/operation_0554 |
|
http://www.geneontology.org/formats/oboInOwl#inSubset
|
http://purl.obolibrary.org/obo/edam#edam |
| http://purl.obolibrary.org/obo/edam#operations
|
|
http://www.w3.org/2000/01/rdf-schema#label
|
Phylogenetic tree analysis (natural selection)
|
|
http://edamontology.org/created_in
|
beta12orEarlier
|
|
http://www.geneontology.org/formats/oboInOwl#hasDefinition
|
Analyse a phylogenetic tree to identify allele frequency distribution and change that is subject to evolutionary pressures (natural selection, genetic drift, mutation and gene flow). Identify type of natural selection (such as stabilizing, balancing or disruptive).
|
|
http://www.w3.org/1999/02/22-rdf-syntax-ns#type
|
http://www.w3.org/2002/07/owl#Class
|
|
http://www.w3.org/2000/01/rdf-schema#comment
|
Stabilizing/purifying (directional) selection favors a single phenotype and tends to decrease genetic diversity as a population stabilizes on a particular trait, selecting out trait extremes or deleterious mutations. In contrast, balancing selection maintain genetic polymorphisms (or multiple alleles), whereas disruptive (or diversifying) selection favors individuals at both extremes of a trait.
|
|
http://www.w3.org/2000/01/rdf-schema#subClassOf
|
http://edamontology.org/operation_0324
|
http://edamontology.org/topic_1811 |
|
http://www.geneontology.org/formats/oboInOwl#hasDbXref
|
VT 1.5.2 Bacteriology
|
|
http://www.w3.org/2000/01/rdf-schema#label
|
Prokaryotes and Archaea
|
|
http://edamontology.org/created_in
|
beta12orEarlier
|
|
http://www.geneontology.org/formats/oboInOwl#consider
|
http://edamontology.org/topic_0621
|
|
http://edamontology.org/oldParent
|
http://edamontology.org/topic_0621
|
|
http://www.geneontology.org/formats/oboInOwl#inSubset
|
http://purl.obolibrary.org/obo/edam#obsolete
|
|
http://www.w3.org/2002/07/owl#deprecated
|
true
|
|
http://www.geneontology.org/formats/oboInOwl#hasDefinition
|
Specific bacteria or archaea, e.g. information on a specific prokaryote genome including molecular sequences, genes and annotation.
|
|
http://edamontology.org/deprecation_comment
|
(jison)Out of EDAM scope. While very useful to have a basic set of IDs for organisms, should find a better way to provide this e.g. in bio.tools (NCBI taxon ID subset).
|
|
http://www.w3.org/1999/02/22-rdf-syntax-ns#type
|
http://www.w3.org/2002/07/owl#Class
|
|
http://www.w3.org/2000/01/rdf-schema#comment
|
The resource may be specific to a prokaryote, a group of prokaryotes or all prokaryotes.
|
|
http://www.w3.org/2000/01/rdf-schema#subClassOf
|
http://www.w3.org/2002/07/owl#DeprecatedClass
|
|
http://edamontology.org/obsolete_since
|
1.17
|
|
http://www.geneontology.org/formats/oboInOwl#hasBroadSynonym
|
Bacteriology
|
http://edamontology.org/topic_0593 |
|
http://www.geneontology.org/formats/oboInOwl#inSubset
|
http://purl.obolibrary.org/obo/edam#events |
| http://purl.obolibrary.org/obo/edam#topics |
| http://purl.obolibrary.org/obo/edam#edam
|
|
http://www.w3.org/2000/01/rdf-schema#label
|
NMR
|
|
http://edamontology.org/created_in
|
beta12orEarlier
|
|
http://www.geneontology.org/formats/oboInOwl#hasNarrowSynonym
|
Nuclear Overhauser Effect Spectroscopy |
| Heteronuclear Overhauser Effect Spectroscopy |
| NOESY |
| HOESY |
| ROESY |
| Rotational Frame Nuclear Overhauser Effect Spectroscopy
|
|
http://www.w3.org/2000/01/rdf-schema#seeAlso
|
https://en.wikipedia.org/wiki/Nuclear_magnetic_resonance_spectroscopy
|
|
http://www.geneontology.org/formats/oboInOwl#hasDefinition
|
An analytical technique that exploits the magenetic properties of certain atomic nuclei to provide information on the structure, dynamics, reaction state and chemical environment of molecules.
|
|
http://www.w3.org/1999/02/22-rdf-syntax-ns#type
|
http://www.w3.org/2002/07/owl#Class
|
|
http://www.geneontology.org/formats/oboInOwl#hasExactSynonym
|
Nuclear magnetic resonance spectroscopy |
| NMR spectroscopy
|
|
http://www.w3.org/2000/01/rdf-schema#subClassOf
|
http://edamontology.org/topic_3382 |
| http://edamontology.org/topic_1317
|
|
http://www.geneontology.org/formats/oboInOwl#hasHumanReadableId
|
NMR
|
|
http://www.geneontology.org/formats/oboInOwl#hasBroadSynonym
|
Spectroscopy
|
http://edamontology.org/data_1099 |
|
http://edamontology.org/regex
|
[A-NR-Z][0-9][A-Z][A-Z0-9][A-Z0-9][0-9]|[OPQ][0-9][A-Z0-9][A-Z0-9][A-Z0-9][0-9]|[A-NR-Z][0-9][A-Z][A-Z0-9][A-Z0-9][0-9].[0-9]+|[OPQ][0-9][A-Z0-9][A-Z0-9][A-Z0-9][0-9].[0-9]+|[A-NR-Z][0-9][A-Z][A-Z0-9][A-Z0-9][0-9]-[0-9]+|[OPQ][0-9][A-Z0-9][A-Z0-9][A-Z0-9][0-9]-[0-9]+
|
|
http://www.geneontology.org/formats/oboInOwl#inSubset
|
http://purl.obolibrary.org/obo/edam#obsolete
|
|
http://www.w3.org/2002/07/owl#deprecated
|
true
|
|
http://www.w3.org/2000/01/rdf-schema#label
|
UniProt accession (extended)
|
|
http://edamontology.org/created_in
|
beta12orEarlier
|
|
http://edamontology.org/example
|
Q7M1G0|P43353-2|P01012.107
|
|
http://www.geneontology.org/formats/oboInOwl#hasDefinition
|
Accession number of a UniProt (protein sequence) database entry. May contain version or isoform number.
|
|
http://www.geneontology.org/formats/oboInOwl#consider
|
http://edamontology.org/data_3021
|
|
http://www.w3.org/1999/02/22-rdf-syntax-ns#type
|
http://www.w3.org/2002/07/owl#Class
|
|
http://www.w3.org/2000/01/rdf-schema#subClassOf
|
http://www.w3.org/2002/07/owl#DeprecatedClass
|
|
http://edamontology.org/obsolete_since
|
1.0
|
http://edamontology.org/data_2315 |
|
http://www.geneontology.org/formats/oboInOwl#inSubset
|
http://purl.obolibrary.org/obo/edam#edam |
| http://purl.obolibrary.org/obo/edam#data |
| http://purl.obolibrary.org/obo/edam#identifiers
|
|
http://www.w3.org/2000/01/rdf-schema#label
|
NCBI version
|
|
http://edamontology.org/created_in
|
beta12orEarlier
|
|
http://www.geneontology.org/formats/oboInOwl#hasDefinition
|
An identifier assigned to sequence records processed by NCBI, made of the accession number of the database record followed by a dot and a version number.
|
|
http://www.w3.org/1999/02/22-rdf-syntax-ns#type
|
http://www.w3.org/2002/07/owl#Class
|
|
http://www.geneontology.org/formats/oboInOwl#hasExactSynonym
|
NCBI accession.version |
| accession.version
|
|
http://www.w3.org/2000/01/rdf-schema#comment
|
Nucleotide sequence version contains two letters followed by six digits, a dot, and a version number (or for older nucleotide sequence records, the format is one letter followed by five digits, a dot, and a version number). Protein sequence version contains three letters followed by five digits, a dot, and a version number.
|
|
http://www.w3.org/2000/01/rdf-schema#subClassOf
|
http://edamontology.org/data_2091 |
| http://edamontology.org/data_2362
|
http://edamontology.org/format_1570 |
|
http://www.geneontology.org/formats/oboInOwl#inSubset
|
http://purl.obolibrary.org/obo/edam#obsolete
|
|
http://www.w3.org/2002/07/owl#deprecated
|
true
|
|
http://www.w3.org/2000/01/rdf-schema#label
|
InterPro entry format
|
|
http://edamontology.org/created_in
|
beta12orEarlier
|
|
http://www.geneontology.org/formats/oboInOwl#hasDefinition
|
Entry format for the InterPro database of protein signatures (sequence classifiers) and classified sequences.
|
|
http://www.geneontology.org/formats/oboInOwl#consider
|
http://edamontology.org/format_2331
|
|
http://www.w3.org/1999/02/22-rdf-syntax-ns#type
|
http://www.w3.org/2002/07/owl#Class
|
|
http://www.w3.org/2000/01/rdf-schema#comment
|
This includes signature metadata, sequence references and a reference to the signature itself. There is normally a header (entry accession numbers and name), abstract, taxonomy information, example proteins etc. Each entry also includes a match list which give a number of different views of the signature matches for the sequences in each InterPro entry.
|
|
http://www.w3.org/2000/01/rdf-schema#subClassOf
|
http://www.w3.org/2002/07/owl#DeprecatedClass
|
|
http://edamontology.org/obsolete_since
|
beta12orEarlier
|
http://edamontology.org/data_1859 |
|
http://www.geneontology.org/formats/oboInOwl#inSubset
|
http://purl.obolibrary.org/obo/edam#edam |
| http://purl.obolibrary.org/obo/edam#data
|
|
http://www.w3.org/2000/01/rdf-schema#label
|
Deletion map
|
|
http://edamontology.org/created_in
|
beta12orEarlier
|
|
http://www.geneontology.org/formats/oboInOwl#hasDefinition
|
A cytogenetic map showing chromosome banding patterns in mutant cell lines relative to the wild type.
|
|
http://www.w3.org/1999/02/22-rdf-syntax-ns#type
|
http://www.w3.org/2002/07/owl#Class
|
|
http://www.geneontology.org/formats/oboInOwl#hasExactSynonym
|
Deletion-based cytogenetic map
|
|
http://www.w3.org/2000/01/rdf-schema#comment
|
A cytogenetic map is built from a set of mutant cell lines with sub-chromosomal deletions and a reference wild-type line ('genome deletion panel'). The panel is used to map markers onto the genome by comparing mutant to wild-type banding patterns. Markers are linked (occur in the same deleted region) if they share the same banding pattern (presence or absence) as the deletion panel.
|
|
http://www.w3.org/2000/01/rdf-schema#subClassOf
|
http://edamontology.org/data_1283
|
http://edamontology.org/data_1872 |
|
http://www.geneontology.org/formats/oboInOwl#inSubset
|
http://purl.obolibrary.org/obo/edam#edam |
| http://purl.obolibrary.org/obo/edam#data |
| http://purl.obolibrary.org/obo/edam#identifiers
|
|
http://www.geneontology.org/formats/oboInOwl#hasDbXref
|
Moby:TaxonName |
| Moby:TaxonScientificName |
| Moby:GCP_Taxon |
| Moby:iANT_organism-xml |
| Moby:TaxonTCS
|
|
http://www.w3.org/2000/01/rdf-schema#label
|
Taxonomic classification
|
|
http://edamontology.org/created_in
|
beta12orEarlier
|
|
http://www.geneontology.org/formats/oboInOwl#hasDefinition
|
The full name for a group of organisms, reflecting their biological classification and (usually) conforming to a standard nomenclature.
|
|
http://www.w3.org/1999/02/22-rdf-syntax-ns#type
|
http://www.w3.org/2002/07/owl#Class
|
|
http://www.geneontology.org/formats/oboInOwl#hasExactSynonym
|
Taxonomic information |
| Taxonomic name
|
|
http://www.w3.org/2000/01/rdf-schema#comment
|
Name components correspond to levels in a taxonomic hierarchy (e.g. 'Genus', 'Species', etc.) Meta information such as a reference where the name was defined and a date might be included.
|
|
http://www.w3.org/2000/01/rdf-schema#subClassOf
|
http://edamontology.org/data_2909
|
http://edamontology.org/topic_0611 |
|
http://www.geneontology.org/formats/oboInOwl#inSubset
|
http://purl.obolibrary.org/obo/edam#events |
| http://purl.obolibrary.org/obo/edam#topics |
| http://purl.obolibrary.org/obo/edam#edam
|
|
http://www.w3.org/2000/01/rdf-schema#label
|
Electron microscopy
|
|
http://edamontology.org/created_in
|
beta12orEarlier
|
|
http://www.geneontology.org/formats/oboInOwl#hasNarrowSynonym
|
Scanning electron microscopy |
| Single particle electron microscopy |
| Electron crystallography |
| Transmission electron microscopy |
| SEM |
| TEM
|
|
http://www.w3.org/2000/01/rdf-schema#seeAlso
|
https://en.wikipedia.org/wiki/Electron_microscope
|
|
http://www.geneontology.org/formats/oboInOwl#hasDefinition
|
The study of matter by studying the interference pattern from firing electrons at a sample, to analyse structures at resolutions higher than can be achieved using light.
|
|
http://www.w3.org/1999/02/22-rdf-syntax-ns#type
|
http://www.w3.org/2002/07/owl#Class
|
|
http://www.w3.org/2000/01/rdf-schema#subClassOf
|
http://edamontology.org/topic_3382 |
| http://edamontology.org/topic_1317
|
|
http://www.geneontology.org/formats/oboInOwl#hasHumanReadableId
|
Electron_microscopy
|
|
http://www.geneontology.org/formats/oboInOwl#hasBroadSynonym
|
Electron diffraction experiment
|
http://edamontology.org/operation_2489 |
|
http://www.geneontology.org/formats/oboInOwl#inSubset
|
http://purl.obolibrary.org/obo/edam#edam |
| http://purl.obolibrary.org/obo/edam#operations
|
|
http://www.w3.org/2000/01/rdf-schema#label
|
Subcellular localisation prediction
|
|
http://edamontology.org/created_in
|
beta12orEarlier
|
|
http://www.w3.org/2000/01/rdf-schema#seeAlso
|
https://en.wikipedia.org/wiki/Subcellular_localization
|
|
http://www.geneontology.org/formats/oboInOwl#hasDefinition
|
Predict the subcellular localisation of a protein sequence.
|
|
http://www.w3.org/1999/02/22-rdf-syntax-ns#type
|
http://www.w3.org/2002/07/owl#Class
|
|
http://www.geneontology.org/formats/oboInOwl#hasExactSynonym
|
Protein targeting prediction |
| Protein subcellular localisation prediction
|
|
http://www.w3.org/2000/01/rdf-schema#comment
|
The prediction might include subcellular localisation (nuclear, cytoplasmic, mitochondrial, chloroplast, plastid, membrane etc) or export (extracellular proteins) of a protein.
|
|
http://www.w3.org/2000/01/rdf-schema#subClassOf
|
_:98 |
| http://edamontology.org/operation_1777
|
http://edamontology.org/operation_3791 |
|
http://www.geneontology.org/formats/oboInOwl#inSubset
|
http://purl.obolibrary.org/obo/edam#edam |
| http://purl.obolibrary.org/obo/edam#operations
|
|
http://www.w3.org/2000/01/rdf-schema#label
|
Collapsing methods
|
|
http://edamontology.org/created_in
|
1.17
|
|
http://www.geneontology.org/formats/oboInOwl#hasDefinition
|
A method whereby data on several variants are "collapsed" into a single covariate based on regions such as genes.
|
|
http://www.w3.org/1999/02/22-rdf-syntax-ns#type
|
http://www.w3.org/2002/07/owl#Class
|
|
http://www.w3.org/2000/01/rdf-schema#comment
|
Genome-wide association studies (GWAS) analyse a genome-wide set of genetic variants in different individuals to see if any variant is associated with a trait. Traditional association techniques can lack the power to detect the significance of rare variants individually, or measure their compound effect (rare variant burden). "Collapsing methods" were developed to overcome these problems.
|
|
http://www.w3.org/2000/01/rdf-schema#subClassOf
|
http://edamontology.org/operation_3197
|
http://edamontology.org/topic_0213 |
|
http://www.geneontology.org/formats/oboInOwl#inSubset
|
http://purl.obolibrary.org/obo/edam#obsolete
|
|
http://www.w3.org/2002/07/owl#deprecated
|
true
|
|
http://www.w3.org/2000/01/rdf-schema#label
|
Mice or rats
|
|
http://edamontology.org/created_in
|
beta12orEarlier
|
|
http://www.geneontology.org/formats/oboInOwl#consider
|
http://edamontology.org/topic_0621
|
|
http://www.geneontology.org/formats/oboInOwl#hasDefinition
|
Information on a specific mouse or rat genome including molecular sequences, genes and annotation.
|
|
http://edamontology.org/deprecation_comment
|
(jison)Out of EDAM scope. While very useful to have a basic set of IDs for organisms, should find a better way to provide this e.g. in bio.tools (NCBI taxon ID subset).
|
|
http://www.w3.org/1999/02/22-rdf-syntax-ns#type
|
http://www.w3.org/2002/07/owl#Class
|
|
http://www.w3.org/2000/01/rdf-schema#comment
|
The resource may be specific to a group of mice / rats or all mice / rats.
|
|
http://edamontology.org/oldParent
|
http://edamontology.org/topic_2820
|
|
http://www.w3.org/2000/01/rdf-schema#subClassOf
|
http://www.w3.org/2002/07/owl#DeprecatedClass
|
|
http://edamontology.org/obsolete_since
|
1.17
|
http://edamontology.org/topic_0209 |
|
http://www.geneontology.org/formats/oboInOwl#inSubset
|
http://purl.obolibrary.org/obo/edam#events |
| http://purl.obolibrary.org/obo/edam#topics |
| http://purl.obolibrary.org/obo/edam#edam
|
|
http://edamontology.org/isdebtag
|
true
|
|
http://www.geneontology.org/formats/oboInOwl#hasDbXref
|
VT 3.1.4 Medicinal chemistry
|
|
http://www.w3.org/2000/01/rdf-schema#label
|
Medicinal chemistry
|
|
http://edamontology.org/created_in
|
beta12orEarlier
|
|
http://www.w3.org/2000/01/rdf-schema#seeAlso
|
https://en.wikipedia.org/wiki/Medicinal_chemistry
|
|
http://www.geneontology.org/formats/oboInOwl#hasDefinition
|
The design and chemical synthesis of bioactive molecules, for example drugs or potential drug compounds, for medicinal purposes.
|
|
http://www.w3.org/1999/02/22-rdf-syntax-ns#type
|
http://www.w3.org/2002/07/owl#Class
|
|
http://www.geneontology.org/formats/oboInOwl#hasExactSynonym
|
Drug design
|
|
http://www.w3.org/2000/01/rdf-schema#comment
|
This includes methods that search compound collections, generate or analyse drug 3D conformations, identify drug targets with structural docking etc.
|
|
http://www.w3.org/2000/01/rdf-schema#subClassOf
|
http://edamontology.org/topic_3371 |
| http://edamontology.org/topic_3336
|
|
http://www.geneontology.org/formats/oboInOwl#hasHumanReadableId
|
Medicinal_chemistry
|
http://edamontology.org/topic_2830 |
|
http://www.geneontology.org/formats/oboInOwl#inSubset
|
http://purl.obolibrary.org/obo/edam#events |
| http://purl.obolibrary.org/obo/edam#topics |
| http://purl.obolibrary.org/obo/edam#edam
|
|
http://www.w3.org/2000/01/rdf-schema#label
|
Immunoproteins, genes and antigens
|
|
http://edamontology.org/created_in
|
beta12orEarlier
|
|
http://www.geneontology.org/formats/oboInOwl#hasNarrowSynonym
|
Antigens |
| Immunogenes |
| Immunopeptides |
| Immunoproteins
|
|
http://www.w3.org/2000/01/rdf-schema#seeAlso
|
https://en.wikipedia.org/wiki/Antigen |
| https://en.wikipedia.org/wiki/Immunoproteins
|
|
http://www.geneontology.org/formats/oboInOwl#hasDefinition
|
Immunity-related genes, proteins and their ligands.
|
|
http://www.w3.org/1999/02/22-rdf-syntax-ns#type
|
http://www.w3.org/2002/07/owl#Class
|
|
http://www.w3.org/2000/01/rdf-schema#comment
|
This includes T cell receptors (TR), major histocompatibility complex (MHC), immunoglobulin superfamily (IgSF) / antibodies, major histocompatibility complex superfamily (MhcSF), etc."
|
|
http://www.geneontology.org/formats/oboInOwl#hasHumanReadableId
|
Immunoproteins_genes_and_antigens
|
|
http://www.w3.org/2000/01/rdf-schema#subClassOf
|
http://edamontology.org/topic_0623 |
| http://edamontology.org/topic_0804
|
http://edamontology.org/operation_0302 |
|
http://www.geneontology.org/formats/oboInOwl#inSubset
|
http://purl.obolibrary.org/obo/edam#edam |
| http://purl.obolibrary.org/obo/edam#operations
|
|
http://www.geneontology.org/formats/oboInOwl#comment
|
This includes sequence-to-3D-profile alignment methods, which align molecular sequence(s) to structural (3D) profile(s) or template(s) (representing a structure or structure alignment) - methods might perform one-to-one, one-to-many or many-to-many comparisons.
|
|
http://www.w3.org/2000/01/rdf-schema#label
|
Protein threading
|
|
http://edamontology.org/created_in
|
beta12orEarlier
|
|
http://www.geneontology.org/formats/oboInOwl#hasNarrowSynonym
|
Sequence-3D profile alignment |
| Sequence-to-3D-profile alignment
|
|
http://www.w3.org/2000/01/rdf-schema#seeAlso
|
https://en.wikipedia.org/wiki/Threading_(protein_sequence)
|
|
http://www.geneontology.org/formats/oboInOwl#hasDefinition
|
Align molecular sequence to structure in 3D space (threading).
|
|
http://www.w3.org/1999/02/22-rdf-syntax-ns#type
|
http://www.w3.org/2002/07/owl#Class
|
|
http://www.geneontology.org/formats/oboInOwl#hasExactSynonym
|
Sequence-structure alignment
|
|
http://www.w3.org/2000/01/rdf-schema#comment
|
Use this concept for methods that evaluate sequence-structure compatibility by assessing residue interactions in 3D. Methods might perform one-to-one, one-to-many or many-to-many comparisons.
|
|
http://www.w3.org/2000/01/rdf-schema#subClassOf
|
_:110 |
| http://edamontology.org/operation_0303 |
| _:111
|
http://edamontology.org/operation_2935 |
|
http://www.geneontology.org/formats/oboInOwl#inSubset
|
http://purl.obolibrary.org/obo/edam#edam |
| http://purl.obolibrary.org/obo/edam#operations
|
|
http://www.geneontology.org/formats/oboInOwl#comment
|
In the case of microarray data, visualise clustered gene expression data as a set of profiles, where each profile shows the gene expression values of a cluster across samples on the X-axis.
|
|
http://www.w3.org/2000/01/rdf-schema#label
|
Clustering profile plotting
|
|
http://edamontology.org/created_in
|
beta12orEarlier
|
|
http://www.geneontology.org/formats/oboInOwl#hasNarrowSynonym
|
Microarray cluster temporal graph rendering |
| Microarray wave graph plotting |
| Microarray wave graph rendering
|
|
http://www.geneontology.org/formats/oboInOwl#hasDefinition
|
Visualise clustered quantitative data as set of different profiles, where each profile is plotted versus different entities or samples on the X-axis.
|
|
http://www.w3.org/1999/02/22-rdf-syntax-ns#type
|
http://www.w3.org/2002/07/owl#Class
|
|
http://www.geneontology.org/formats/oboInOwl#hasExactSynonym
|
Clustered quantitative data rendering |
| Wave graph plotting |
| Clustered quantitative data plotting
|
|
http://www.w3.org/2000/01/rdf-schema#subClassOf
|
http://edamontology.org/operation_0571
|
http://edamontology.org/operation_2939 |
|
http://www.geneontology.org/formats/oboInOwl#inSubset
|
http://purl.obolibrary.org/obo/edam#edam |
| http://purl.obolibrary.org/obo/edam#operations
|
|
http://www.geneontology.org/formats/oboInOwl#comment
|
Examples for visualization are the distribution of variance over the components, loading and score plots.
|
|
http://www.w3.org/2000/01/rdf-schema#label
|
Principal component visualisation
|
|
http://edamontology.org/created_in
|
beta12orEarlier
|
|
http://www.geneontology.org/formats/oboInOwl#hasNarrowSynonym
|
Microarray principal component rendering |
| ED visualization |
| PCA visualization |
| Essential Dynamics visualization |
| Principal modes visualization |
| Microarray principal component plotting
|
|
http://www.geneontology.org/formats/oboInOwl#hasDefinition
|
Visualize the results of a principal component analysis (orthogonal data transformation). For example, visualization of the principal components (essential subspace) coming from a Principal Component Analysis (PCA) on the trajectory atomistic coordinates of a molecular structure.
|
|
http://www.w3.org/1999/02/22-rdf-syntax-ns#type
|
http://www.w3.org/2002/07/owl#Class
|
|
http://www.geneontology.org/formats/oboInOwl#hasExactSynonym
|
Principal component plotting |
| PCA plotting
|
|
http://www.w3.org/2000/01/rdf-schema#comment
|
The use of Principal Component Analysis (PCA), a multivariate statistical analysis to obtain collective variables on the atomic positional fluctuations, helps to separate the configurational space in two subspaces: an “essential” subspace containing relevant motions, and another one containing irrelevant local fluctuations.
|
|
http://www.w3.org/2000/01/rdf-schema#subClassOf
|
http://edamontology.org/operation_0337
|
http://edamontology.org/operation_2937 |
|
http://www.geneontology.org/formats/oboInOwl#inSubset
|
http://purl.obolibrary.org/obo/edam#edam |
| http://purl.obolibrary.org/obo/edam#operations
|
|
http://www.w3.org/2000/01/rdf-schema#label
|
Proximity map plotting
|
|
http://edamontology.org/created_in
|
beta12orEarlier
|
|
http://www.geneontology.org/formats/oboInOwl#hasNarrowSynonym
|
Microarray proximity map rendering |
| Microarray distance map rendering |
| Microarray proximity map plotting |
| Correlation matrix rendering |
| Correlation matrix plotting
|
|
http://www.geneontology.org/formats/oboInOwl#hasDefinition
|
Generate a plot of distances (distance or correlation matrix) between expression values.
|
|
http://www.w3.org/1999/02/22-rdf-syntax-ns#type
|
http://www.w3.org/2002/07/owl#Class
|
|
http://www.geneontology.org/formats/oboInOwl#hasExactSynonym
|
Distance matrix rendering |
| Distance matrix plotting |
| Distance map rendering |
| Proximity map rendering
|
|
http://www.w3.org/2000/01/rdf-schema#subClassOf
|
http://edamontology.org/operation_0571
|
http://edamontology.org/operation_2943 |
|
http://www.geneontology.org/formats/oboInOwl#inSubset
|
http://purl.obolibrary.org/obo/edam#edam |
| http://purl.obolibrary.org/obo/edam#operations
|
|
http://www.geneontology.org/formats/oboInOwl#comment
|
In the case of micorarray data, visualise raw and pre-processed gene expression data, via a plot showing over- and under-expression along with mean, upper and lower quartiles.
|
|
http://www.w3.org/2000/01/rdf-schema#label
|
Box-Whisker plot plotting
|
|
http://edamontology.org/created_in
|
beta12orEarlier
|
|
http://www.geneontology.org/formats/oboInOwl#hasNarrowSynonym
|
Microarray Box-Whisker plot plotting
|
|
http://www.w3.org/2000/01/rdf-schema#seeAlso
|
https://en.wikipedia.org/wiki/Box_plot
|
|
http://www.geneontology.org/formats/oboInOwl#hasDefinition
|
Generate a box plot, i.e. a depiction of groups of numerical data through their quartiles.
|
|
http://www.w3.org/1999/02/22-rdf-syntax-ns#type
|
http://www.w3.org/2002/07/owl#Class
|
|
http://www.geneontology.org/formats/oboInOwl#hasExactSynonym
|
Box plot plotting
|
|
http://www.w3.org/2000/01/rdf-schema#subClassOf
|
http://edamontology.org/operation_0337
|
http://edamontology.org/topic_3365 |
|
http://www.geneontology.org/formats/oboInOwl#inSubset
|
http://purl.obolibrary.org/obo/edam#events |
| http://purl.obolibrary.org/obo/edam#topics |
| http://purl.obolibrary.org/obo/edam#edam
|
|
http://www.w3.org/2000/01/rdf-schema#label
|
Data architecture, analysis and design
|
|
http://edamontology.org/created_in
|
1.4
|
|
http://www.geneontology.org/formats/oboInOwl#hasNarrowSynonym
|
Data analysis |
| Data architecture |
| Data design
|
|
http://www.w3.org/2000/01/rdf-schema#seeAlso
|
https://en.wikipedia.org/wiki/Data_architecture
|
|
http://www.geneontology.org/formats/oboInOwl#hasDefinition
|
The development of policies, models and standards that cover data acquisition, storage and integration, such that it can be put to use, typically through a process of systematically applying statistical and / or logical techniques to describe, illustrate, summarise or evaluate data.
|
|
http://www.w3.org/1999/02/22-rdf-syntax-ns#type
|
http://www.w3.org/2002/07/owl#Class
|
|
http://www.geneontology.org/formats/oboInOwl#hasHumanReadableId
|
Data_architecture_analysis_and_design
|
|
http://www.w3.org/2000/01/rdf-schema#subClassOf
|
http://edamontology.org/topic_3071
|
http://edamontology.org/operation_0327 |
|
http://www.geneontology.org/formats/oboInOwl#inSubset
|
http://purl.obolibrary.org/obo/edam#edam |
| http://purl.obolibrary.org/obo/edam#operations
|
|
http://www.w3.org/2000/01/rdf-schema#label
|
Phylogenetic footprinting / shadowing
|
|
http://edamontology.org/created_in
|
beta12orEarlier
|
|
http://www.geneontology.org/formats/oboInOwl#hasDefinition
|
Infer a phylogenetic tree by comparing orthologous sequences in different species, particularly many closely related species (phylogenetic shadowing).
|
|
http://www.w3.org/1999/02/22-rdf-syntax-ns#type
|
http://www.w3.org/2002/07/owl#Class
|
|
http://www.w3.org/2000/01/rdf-schema#comment
|
A phylogenetic 'shadow' represents the additive differences between individual sequences. By masking or 'shadowing' variable positions a conserved sequence is produced with few or none of the variations, which is then compared to the sequences of interest to identify significant regions of conservation.
|
|
http://www.w3.org/2000/01/rdf-schema#subClassOf
|
http://edamontology.org/operation_0540 |
| _:126
|
http://edamontology.org/operation_0384 |
|
http://www.geneontology.org/formats/oboInOwl#inSubset
|
http://purl.obolibrary.org/obo/edam#edam |
| http://purl.obolibrary.org/obo/edam#operations
|
|
http://www.geneontology.org/formats/oboInOwl#hasDbXref
|
WHATIF:AtomAccessibilitySolventPlus |
| WHATIF:AtomAccessibilitySolvent
|
|
http://www.w3.org/2000/01/rdf-schema#label
|
Accessible surface calculation
|
|
http://edamontology.org/created_in
|
beta12orEarlier
|
|
http://www.geneontology.org/formats/oboInOwl#hasNarrowSynonym
|
Protein solvent accessibility calculation
|
|
http://www.geneontology.org/formats/oboInOwl#hasDefinition
|
Calculate solvent accessible or buried surface areas in protein or other molecular structures.
|
|
http://www.w3.org/1999/02/22-rdf-syntax-ns#type
|
http://www.w3.org/2002/07/owl#Class
|
|
http://www.w3.org/2000/01/rdf-schema#comment
|
Solvent accessibility might be calculated for the backbone, sidechain and total (backbone plus sidechain).
|
|
http://www.w3.org/2000/01/rdf-schema#subClassOf
|
http://edamontology.org/operation_3351 |
| _:132
|
http://edamontology.org/has_format |
|
http://purl.obolibrary.org/obo/is_anti_symmetric
|
false
|
|
http://www.w3.org/2000/01/rdf-schema#label
|
has format
|
|
http://purl.obolibrary.org/obo/is_reflexive
|
false
|
|
http://www.geneontology.org/formats/oboInOwl#isCyclic
|
false
|
|
http://www.geneontology.org/formats/oboInOwl#inSubset
|
edam |
| relations
|
|
http://www.w3.org/2000/01/rdf-schema#range
|
http://edamontology.org/format_1915
|
|
http://purl.obolibrary.org/obo/is_symmetric
|
false
|
|
http://www.w3.org/2000/01/rdf-schema#domain
|
http://edamontology.org/data_0006
|
|
http://www.w3.org/2002/07/owl#inverseOf
|
http://edamontology.org/is_format_of
|
|
http://www.w3.org/2000/01/rdf-schema#seeAlso
|
http://www.loa-cnr.it/ontologies/DOLCE-Lite.owl#has-quality" |
| "http://purl.obolibrary.org/obo/OBI_0000298"
|
|
http://www.geneontology.org/formats/oboInOwl#hasDefinition
|
'A has_format B' defines for the subject A, that it has the object B as its data format.
|
|
http://www.w3.org/1999/02/22-rdf-syntax-ns#type
|
http://www.w3.org/2002/07/owl#ObjectProperty
|
|
http://www.w3.org/2000/01/rdf-schema#comment
|
Subject A can be any concept or entity outside of an ontology (or an ontology concept in a role of an entity being semantically annotated) that is (or is in a role of) 'Data', or an input, output, input or output argument of an 'Operation'. Object B can either be a concept that is a 'Format', or in unexpected cases an entity outside of an ontology that is a 'Format' or is in the role of a 'Format'. In EDAM, 'has_format' is not explicitly defined between EDAM concepts, only the inverse 'is_format_of'.
|
|
http://purl.obolibrary.org/obo/transitive_over
|
OBO_REL:is_a
|
http://edamontology.org/operation_3458 |
|
http://www.geneontology.org/formats/oboInOwl#inSubset
|
http://purl.obolibrary.org/obo/edam#edam |
| http://purl.obolibrary.org/obo/edam#operations
|
|
http://edamontology.org/is_refactor_candidate
|
true
|
|
http://www.w3.org/2000/01/rdf-schema#label
|
Single particle alignment and classification
|
|
http://edamontology.org/created_in
|
1.7
|
|
http://www.geneontology.org/formats/oboInOwl#hasDefinition
|
Compare (align and classify) multiple particle images from a micrograph in order to produce a representative image of the particle.
|
|
http://www.w3.org/1999/02/22-rdf-syntax-ns#type
|
http://www.w3.org/2002/07/owl#Class
|
|
http://www.w3.org/2000/01/rdf-schema#comment
|
A micrograph can include particles in multiple different orientations and/or conformations. Particles are compared and organised into sets based on their similarity. Typically iterations of classification and alignment and are performed to optimise the final 3D EM map.
|
|
http://edamontology.org/refactor_comment
|
This is two related concepts.
|
|
http://www.w3.org/2000/01/rdf-schema#subClassOf
|
http://edamontology.org/operation_3457 |
| http://edamontology.org/operation_2990
|
http://edamontology.org/data_1722 |
|
http://www.geneontology.org/formats/oboInOwl#inSubset
|
http://purl.obolibrary.org/obo/edam#obsolete
|
|
http://www.w3.org/2002/07/owl#deprecated
|
true
|
|
http://www.w3.org/2000/01/rdf-schema#label
|
FMA
|
|
http://edamontology.org/created_in
|
beta12orEarlier
|
|
http://www.geneontology.org/formats/oboInOwl#hasDefinition
|
A term from Foundational Model of Anatomy.
|
|
http://www.geneontology.org/formats/oboInOwl#consider
|
http://edamontology.org/data_0966
|
|
http://www.w3.org/1999/02/22-rdf-syntax-ns#type
|
http://www.w3.org/2002/07/owl#Class
|
|
http://www.w3.org/2000/01/rdf-schema#comment
|
Classifies anatomical entities according to their shared characteristics (genus) and distinguishing characteristics (differentia). Specifies the part-whole and spatial relationships of the entities, morphological transformation of the entities during prenatal development and the postnatal life cycle and principles, rules and definitions according to which classes and relationships in the other three components of FMA are represented.
|
|
http://www.w3.org/2000/01/rdf-schema#subClassOf
|
http://www.w3.org/2002/07/owl#DeprecatedClass
|
|
http://edamontology.org/obsolete_since
|
beta12orEarlier
|
http://edamontology.org/topic_3474 |
|
http://www.geneontology.org/formats/oboInOwl#inSubset
|
http://purl.obolibrary.org/obo/edam#topics |
| http://purl.obolibrary.org/obo/edam#edam
|
|
http://www.geneontology.org/formats/oboInOwl#hasDbXref
|
VT 1.2.2 Artificial Intelligence (expert systems, machine learning, robotics)
|
|
http://www.w3.org/2000/01/rdf-schema#label
|
Machine learning
|
|
http://edamontology.org/created_in
|
1.7
|
|
http://www.geneontology.org/formats/oboInOwl#hasNarrowSynonym
|
Unsupervised learning |
| Kernel methods |
| Neural networks |
| Reinforcement learning |
| Recommender system |
| Ensembl learning |
| Supervised learning |
| Knowledge representation |
| Active learning
|
|
http://www.w3.org/2000/01/rdf-schema#seeAlso
|
https://en.wikipedia.org/wiki/Machine_learning
|
|
http://www.geneontology.org/formats/oboInOwl#hasDefinition
|
A topic concerning the application of artificial intelligence methods to algorithms, in order to create methods that can learn from data in order to generate an ouput, rather than relying on explicitly encoded information only.
|
|
http://www.w3.org/1999/02/22-rdf-syntax-ns#type
|
http://www.w3.org/2002/07/owl#Class
|
|
http://www.w3.org/2000/01/rdf-schema#subClassOf
|
http://edamontology.org/topic_3316
|
|
http://www.geneontology.org/formats/oboInOwl#hasHumanReadableId
|
Machine_learning
|
|
http://www.geneontology.org/formats/oboInOwl#hasBroadSynonym
|
Artificial Intelligence
|
http://edamontology.org/format_3556 |
|
http://www.geneontology.org/formats/oboInOwl#hasDbXref
|
http://www.iana.org/assignments/media-types/multipart/related |
| https://en.wikipedia.org/wiki/MHTML |
| https://tools.ietf.org/html/rfc2557
|
|
http://edamontology.org/media_type
|
http://www.iana.org/assignments/media-types/multipart/related
|
|
http://www.w3.org/2000/01/rdf-schema#label
|
MHTML
|
|
http://edamontology.org/created_in
|
1.9
|
|
http://edamontology.org/documentation
|
https://tools.ietf.org/html/rfc2557
|
|
http://www.geneontology.org/formats/oboInOwl#hasExactSynonym
|
HTML email message format |
| MHTML format |
| MHT format |
| HTML email format |
| MHT |
| MIME HTML format |
| MIME HTML
|
|
http://www.geneontology.org/formats/oboInOwl#inSubset
|
http://purl.obolibrary.org/obo/edam#formats |
| http://purl.obolibrary.org/obo/edam#edam
|
|
http://www.geneontology.org/formats/oboInOwl#comment
|
MHTML is not strictly an HTML format, it is encoded as an HTML email message (although with multipart/related instead of multipart/alternative). It, however, contains the main HTML block as its core, and thus it is for practical reasons incuded in EDAM as a specialisation of 'HTML'.
|
|
http://edamontology.org/file_extension
|
mhtml|mht|eml
|
|
http://www.geneontology.org/formats/oboInOwl#hasDefinition
|
MIME HTML format for Web pages, which can include external resources, including images, Flash animations and so on.
|
|
http://www.w3.org/1999/02/22-rdf-syntax-ns#type
|
http://www.w3.org/2002/07/owl#Class
|
|
http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym
|
MIME multipart |
| MIME multipart format |
| MIME multipart message |
| MIME multipart message format
|
|
http://www.w3.org/2000/01/rdf-schema#subClassOf
|
http://edamontology.org/format_2331
|
http://edamontology.org/operation_1820 |
|
http://www.geneontology.org/formats/oboInOwl#inSubset
|
http://purl.obolibrary.org/obo/edam#obsolete
|
|
http://www.w3.org/2002/07/owl#deprecated
|
true
|
|
http://www.w3.org/2000/01/rdf-schema#label
|
Protein residue surface calculation (vacuum accessible)
|
|
http://edamontology.org/created_in
|
beta12orEarlier
|
|
http://www.geneontology.org/formats/oboInOwl#hasDefinition
|
Calculate the solvent accessibility ('vacuum accessible surface') for each residue in a structure. This is the accessibility of the residue when taken out of the protein together with the backbone atoms of any residue it is covalently bound to.
|
|
http://www.w3.org/1999/02/22-rdf-syntax-ns#type
|
http://www.w3.org/2002/07/owl#Class
|
|
http://www.geneontology.org/formats/oboInOwl#replacedBy
|
http://edamontology.org/operation_0387
|
|
http://www.w3.org/2000/01/rdf-schema#comment
|
Solvent accessibility might be calculated for the backbone, sidechain and total (backbone plus sidechain).
|
|
http://www.w3.org/2000/01/rdf-schema#subClassOf
|
http://www.w3.org/2002/07/owl#DeprecatedClass
|
|
http://edamontology.org/obsolete_since
|
1.12
|
http://edamontology.org/operation_1822 |
|
http://www.geneontology.org/formats/oboInOwl#inSubset
|
http://purl.obolibrary.org/obo/edam#obsolete
|
|
http://www.w3.org/2002/07/owl#deprecated
|
true
|
|
http://www.w3.org/2000/01/rdf-schema#label
|
Protein residue surface calculation (vacuum molecular)
|
|
http://edamontology.org/created_in
|
beta12orEarlier
|
|
http://www.geneontology.org/formats/oboInOwl#hasDefinition
|
Calculate the solvent accessibility ('vacuum molecular surface') for each residue in a structure. This is the accessibility of the residue when taken out of the protein together with the backbone atoms of any residue it is covalently bound to.
|
|
http://www.w3.org/1999/02/22-rdf-syntax-ns#type
|
http://www.w3.org/2002/07/owl#Class
|
|
http://www.geneontology.org/formats/oboInOwl#replacedBy
|
http://edamontology.org/operation_0387
|
|
http://www.w3.org/2000/01/rdf-schema#comment
|
Solvent accessibility might be calculated for the backbone, sidechain and total (backbone plus sidechain).
|
|
http://www.w3.org/2000/01/rdf-schema#subClassOf
|
http://www.w3.org/2002/07/owl#DeprecatedClass
|
|
http://edamontology.org/obsolete_since
|
1.12
|
http://edamontology.org/has_identifier |
|
http://purl.obolibrary.org/obo/is_anti_symmetric
|
false
|
|
http://www.w3.org/2000/01/rdf-schema#label
|
has identifier
|
|
http://purl.obolibrary.org/obo/is_reflexive
|
false
|
|
http://www.geneontology.org/formats/oboInOwl#isCyclic
|
false
|
|
http://www.geneontology.org/formats/oboInOwl#inSubset
|
edam |
| relations
|
|
http://www.w3.org/2000/01/rdf-schema#range
|
http://edamontology.org/data_0842
|
|
http://purl.obolibrary.org/obo/is_symmetric
|
false
|
|
http://www.w3.org/2000/01/rdf-schema#domain
|
http://edamontology.org/data_0006
|
|
http://www.w3.org/2002/07/owl#inverseOf
|
http://edamontology.org/is_identifier_of
|
|
http://www.geneontology.org/formats/oboInOwl#hasDefinition
|
'A has_identifier B' defines for the subject A, that it has the object B as its identifier.
|
|
http://www.w3.org/1999/02/22-rdf-syntax-ns#type
|
http://www.w3.org/2002/07/owl#ObjectProperty
|
|
http://www.w3.org/2000/01/rdf-schema#comment
|
Subject A can be any concept or entity outside of an ontology (or an ontology concept in a role of an entity being semantically annotated). Object B can either be a concept that is an 'Identifier', or an entity outside of an ontology that is an 'Identifier' or is in the role of an 'Identifier'. In EDAM, 'has_identifier' is not explicitly defined between EDAM concepts, only the inverse 'is_identifier_of'.
|
|
http://purl.obolibrary.org/obo/transitive_over
|
OBO_REL:is_a
|
http://edamontology.org/operation_0417 |
|
http://www.geneontology.org/formats/oboInOwl#inSubset
|
http://purl.obolibrary.org/obo/edam#edam |
| http://purl.obolibrary.org/obo/edam#operations
|
|
http://www.w3.org/2000/01/rdf-schema#label
|
Post-translation modification site prediction
|
|
http://edamontology.org/created_in
|
beta12orEarlier
|
|
http://www.geneontology.org/formats/oboInOwl#hasNarrowSynonym
|
Pupylation prediction |
| Hydroxylation site prediction |
| N-myristoylation prediction |
| GPI modification site prediction |
| Phosphoglycerylation prediction |
| Sulfation site prediction |
| Prenylation prediction |
| GPI anchor site prediction |
| Prenylation site prediction |
| Dephosphorylation site prediction |
| Pupylation site prediction |
| Tyrosine nitration prediction |
| S-nitrosylation site prediction |
| Tyrosine nitration site prediction |
| S-sulfenylation site prediction |
| Succinylation prediction |
| GPI modification prediction |
| Ubiquitination prediction |
| Sumoylation prediction |
| Ubiquitination site prediction |
| Hydroxylation prediction |
| Phosphorylation site prediction |
| GPI anchor prediction |
| Glycosylation site prediction |
| Dephosphorylation prediction |
| Phosphoglycerylation site prediction |
| Palmitoylation site prediction |
| S-nitrosylation prediction |
| Glycosylation prediction |
| N-terminal myristoylation site prediction |
| Acetylation site prediction |
| Sulfation prediction |
| Acetylation prediction |
| Succinylation site prediction |
| S-sulfenylation prediction |
| Methylation prediction |
| N-terminal myristoylation prediction |
| N-myristoylation site prediction |
| Sumoylation site prediction |
| Phosphorylation prediction |
| N-terminal acetylation prediction |
| Palmitoylation prediction |
| Methylation site prediction |
| N-terminal acetylation site prediction
|
|
http://www.geneontology.org/formats/oboInOwl#hasDefinition
|
Predict post-translation modification sites in protein sequences.
|
|
http://www.w3.org/1999/02/22-rdf-syntax-ns#type
|
http://www.w3.org/2002/07/owl#Class
|
|
http://www.geneontology.org/formats/oboInOwl#hasExactSynonym
|
PTM site analysis |
| PTM analysis |
| PTM site prediction |
| Protein post-translation modification site prediction |
| PTM prediction
|
|
http://www.w3.org/2000/01/rdf-schema#comment
|
Methods might predict sites of methylation, N-terminal myristoylation, N-terminal acetylation, sumoylation, palmitoylation, phosphorylation, sulfation, glycosylation, glycosylphosphatidylinositol (GPI) modification sites (GPI lipid anchor signals) etc.
|
|
http://www.w3.org/2000/01/rdf-schema#subClassOf
|
_:150 |
| http://edamontology.org/operation_3092
|
http://edamontology.org/operation_0426 |
|
http://www.geneontology.org/formats/oboInOwl#inSubset
|
http://purl.obolibrary.org/obo/edam#obsolete
|
|
http://www.w3.org/2002/07/owl#deprecated
|
true
|
|
http://www.w3.org/2000/01/rdf-schema#label
|
Gene component prediction
|
|
http://edamontology.org/created_in
|
beta12orEarlier
|
|
http://www.geneontology.org/formats/oboInOwl#hasDefinition
|
Detect, predict and identify genetic elements such as promoters, coding regions, splice sites, etc in DNA sequences.
|
|
http://www.w3.org/1999/02/22-rdf-syntax-ns#type
|
http://www.w3.org/2002/07/owl#Class
|
|
http://www.geneontology.org/formats/oboInOwl#replacedBy
|
http://edamontology.org/operation_2454
|
|
http://www.w3.org/2000/01/rdf-schema#comment
|
Methods for gene prediction might be ab initio, based on phylogenetic comparisons, use motifs, sequence features, support vector machine, alignment etc.
|
|
http://www.w3.org/2000/01/rdf-schema#subClassOf
|
http://www.w3.org/2002/07/owl#DeprecatedClass
|
|
http://edamontology.org/obsolete_since
|
1.12
|
http://edamontology.org/data_2974 |
|
http://www.geneontology.org/formats/oboInOwl#inSubset
|
http://purl.obolibrary.org/obo/edam#obsolete
|
|
http://www.w3.org/2002/07/owl#deprecated
|
true
|
|
http://www.w3.org/2000/01/rdf-schema#label
|
Protein sequence (raw)
|
|
http://edamontology.org/created_in
|
beta12orEarlier
|
|
http://www.geneontology.org/formats/oboInOwl#hasDefinition
|
A raw protein sequence (string of characters).
|
|
http://edamontology.org/deprecation_comment
|
Deprecated because this is bloat / confusing & better handled as an EDAM Format concept - "raw" sequences just imply a particular format (i.e. one with a vanilla string, possible in a particular alphabet, with no metadata).
|
|
http://www.w3.org/1999/02/22-rdf-syntax-ns#type
|
http://www.w3.org/2002/07/owl#Class
|
|
http://www.geneontology.org/formats/oboInOwl#replacedBy
|
http://edamontology.org/data_2976
|
|
http://www.geneontology.org/formats/oboInOwl#hasExactSynonym
|
Raw protein sequence |
| Raw amino acid sequences |
| Raw sequence (protein) |
| Raw amino acid sequence
|
|
http://edamontology.org/oldParent
|
http://edamontology.org/data_0848
|
|
http://www.w3.org/2000/01/rdf-schema#subClassOf
|
http://www.w3.org/2002/07/owl#DeprecatedClass
|
|
http://edamontology.org/obsolete_since
|
1.23
|
http://edamontology.org/data_1664 |
|
http://www.geneontology.org/formats/oboInOwl#inSubset
|
http://purl.obolibrary.org/obo/edam#obsolete
|
|
http://www.w3.org/2002/07/owl#deprecated
|
true
|
|
http://www.w3.org/2000/01/rdf-schema#label
|
MIRIAM datatype
|
|
http://edamontology.org/created_in
|
beta12orEarlier
|
|
http://www.geneontology.org/formats/oboInOwl#consider
|
http://edamontology.org/data_1883
|
|
http://www.geneontology.org/formats/oboInOwl#hasDefinition
|
An entry (data type) from the Minimal Information Requested in the Annotation of Biochemical Models (MIRIAM) database of data resources.
|
|
http://www.w3.org/1999/02/22-rdf-syntax-ns#type
|
http://www.w3.org/2002/07/owl#Class
|
|
http://www.w3.org/2000/01/rdf-schema#comment
|
A MIRIAM entry describes a MIRIAM data type including the official name, synonyms, root URI, identifier pattern (regular expression applied to a unique identifier of the data type) and documentation. Each data type can be associated with several resources. Each resource is a physical location of a service (typically a database) providing information on the elements of a data type. Several resources may exist for each data type, provided the same (mirrors) or different information. MIRIAM provides a stable and persistent reference to its data types.
|
|
http://www.w3.org/2000/01/rdf-schema#subClassOf
|
http://www.w3.org/2002/07/owl#DeprecatedClass
|
|
http://edamontology.org/obsolete_since
|
1.5
|
http://edamontology.org/data_1667 |
|
http://www.geneontology.org/formats/oboInOwl#inSubset
|
http://purl.obolibrary.org/obo/edam#edam |
| http://purl.obolibrary.org/obo/edam#data
|
|
http://www.w3.org/2000/01/rdf-schema#label
|
E-value
|
|
http://edamontology.org/created_in
|
beta12orEarlier
|
|
http://www.geneontology.org/formats/oboInOwl#hasDefinition
|
A simple floating point number defining the lower or upper limit of an expectation value (E-value).
|
|
http://www.w3.org/1999/02/22-rdf-syntax-ns#type
|
http://www.w3.org/2002/07/owl#Class
|
|
http://www.geneontology.org/formats/oboInOwl#hasExactSynonym
|
Expectation value
|
|
http://www.w3.org/2000/01/rdf-schema#comment
|
An expectation value (E-Value) is the expected number of observations which are at least as extreme as observations expected to occur by random chance. The E-value describes the number of hits with a given score or better that are expected to occur at random when searching a database of a particular size. It decreases exponentially with the score (S) of a hit. A low E value indicates a more significant score.
|
|
http://www.w3.org/2000/01/rdf-schema#subClassOf
|
http://edamontology.org/data_0951
|
http://edamontology.org/operation_0430 |
|
http://www.geneontology.org/formats/oboInOwl#inSubset
|
http://purl.obolibrary.org/obo/edam#edam |
| http://purl.obolibrary.org/obo/edam#operations
|
|
http://www.w3.org/2000/01/rdf-schema#label
|
CpG island and isochore detection
|
|
http://edamontology.org/created_in
|
beta12orEarlier
|
|
http://www.geneontology.org/formats/oboInOwl#hasDefinition
|
Find CpG rich regions in a nucleotide sequence or isochores in genome sequences.
|
|
http://www.w3.org/1999/02/22-rdf-syntax-ns#type
|
http://www.w3.org/2002/07/owl#Class
|
|
http://www.geneontology.org/formats/oboInOwl#hasExactSynonym
|
CpG island and isochores detection |
| CpG island and isochores rendering
|
|
http://www.w3.org/2000/01/rdf-schema#comment
|
An isochore is long region (> 3 KB) of DNA with very uniform GC content, in contrast to the rest of the genome. Isochores tend tends to have more genes, higher local melting or denaturation temperatures, and different flexibility. Methods might calculate fractional GC content or variation of GC content, predict methylation status of CpG islands etc. This includes methods that visualise CpG rich regions in a nucleotide sequence, for example plot isochores in a genome sequence.
|
|
http://www.w3.org/2000/01/rdf-schema#subClassOf
|
_:164 |
| http://edamontology.org/operation_0415
|
http://edamontology.org/data_1675 |
|
http://www.geneontology.org/formats/oboInOwl#inSubset
|
http://purl.obolibrary.org/obo/edam#obsolete
|
|
http://www.w3.org/2002/07/owl#deprecated
|
true
|
|
http://www.w3.org/2000/01/rdf-schema#label
|
Job status
|
|
http://edamontology.org/created_in
|
beta12orEarlier
|
|
http://www.geneontology.org/formats/oboInOwl#hasDefinition
|
Metadata on the status of a submitted job.
|
|
http://www.geneontology.org/formats/oboInOwl#consider
|
http://edamontology.org/data_3106
|
|
http://www.w3.org/1999/02/22-rdf-syntax-ns#type
|
http://www.w3.org/2002/07/owl#Class
|
|
http://www.w3.org/2000/01/rdf-schema#comment
|
Values for EBI services are 'DONE' (job has finished and the results can then be retrieved), 'ERROR' (the job failed or no results where found), 'NOT_FOUND' (the job id is no longer available; job results might be deleted, 'PENDING' (the job is in a queue waiting processing), 'RUNNING' (the job is currently being processed).
|
|
http://www.w3.org/2000/01/rdf-schema#subClassOf
|
http://www.w3.org/2002/07/owl#DeprecatedClass
|
|
http://edamontology.org/obsolete_since
|
1.5
|
http://edamontology.org/operation_0448 |
|
http://www.geneontology.org/formats/oboInOwl#inSubset
|
http://purl.obolibrary.org/obo/edam#edam |
| http://purl.obolibrary.org/obo/edam#operations
|
|
http://www.w3.org/2000/01/rdf-schema#label
|
Sequence alignment analysis (conservation)
|
|
http://edamontology.org/created_in
|
beta12orEarlier
|
|
http://www.geneontology.org/formats/oboInOwl#hasDefinition
|
Analyse character conservation in a molecular sequence alignment, for example to derive a consensus sequence.
|
|
http://www.w3.org/1999/02/22-rdf-syntax-ns#type
|
http://www.w3.org/2002/07/owl#Class
|
|
http://www.geneontology.org/formats/oboInOwl#hasExactSynonym
|
Residue conservation analysis
|
|
http://www.w3.org/2000/01/rdf-schema#comment
|
Use this concept for methods that calculate substitution rates, estimate relative site variability, identify sites with biased properties, derive a consensus sequence, or identify highly conserved or very poorly conserved sites, regions, blocks etc.
|
|
http://www.w3.org/2000/01/rdf-schema#subClassOf
|
http://edamontology.org/operation_0258
|
http://edamontology.org/operation_0499 |
|
http://www.geneontology.org/formats/oboInOwl#inSubset
|
http://purl.obolibrary.org/obo/edam#edam |
| http://purl.obolibrary.org/obo/edam#operations
|
|
http://www.w3.org/2000/01/rdf-schema#label
|
Tree-based sequence alignment
|
|
http://edamontology.org/created_in
|
beta12orEarlier
|
|
http://www.geneontology.org/formats/oboInOwl#hasDefinition
|
Align multiple sequences using relative gap costs calculated from neighbors in a supplied phylogenetic tree.
|
|
http://www.w3.org/1999/02/22-rdf-syntax-ns#type
|
http://www.w3.org/2002/07/owl#Class
|
|
http://www.geneontology.org/formats/oboInOwl#hasExactSynonym
|
Phylogenetic tree-based multiple sequence alignment construction |
| Sequence alignment (phylogenetic tree-based) |
| Sequence alignment generation (phylogenetic tree-based) |
| Multiple sequence alignment (phylogenetic tree-based) |
| Multiple sequence alignment construction (phylogenetic tree-based)
|
|
http://www.w3.org/2000/01/rdf-schema#comment
|
This is supposed to give a more biologically meaningful alignment than standard alignments.
|
|
http://www.w3.org/2000/01/rdf-schema#subClassOf
|
_:171 |
| http://edamontology.org/operation_0292
|
http://edamontology.org/operation_0487 |
|
http://www.geneontology.org/formats/oboInOwl#inSubset
|
http://purl.obolibrary.org/obo/edam#edam |
| http://purl.obolibrary.org/obo/edam#operations
|
|
http://www.w3.org/2000/01/rdf-schema#label
|
Haplotype mapping
|
|
http://edamontology.org/created_in
|
beta12orEarlier
|
|
http://www.geneontology.org/formats/oboInOwl#hasDefinition
|
Infer haplotypes, either alleles at multiple loci that are transmitted together on the same chromosome, or a set of single nucleotide polymorphisms (SNPs) on a single chromatid that are statistically associated.
|
|
http://www.w3.org/1999/02/22-rdf-syntax-ns#type
|
http://www.w3.org/2002/07/owl#Class
|
|
http://www.geneontology.org/formats/oboInOwl#hasExactSynonym
|
Haplotype inference |
| Haplotype reconstruction |
| Haplotype map generation
|
|
http://www.w3.org/2000/01/rdf-schema#comment
|
Haplotype inference can help in population genetic studies and the identification of complex disease genes, , and is typically based on aligned single nucleotide polymorphism (SNP) fragments. Haplotype comparison is a useful way to characterize the genetic variation between individuals. An individual's haplotype describes which nucleotide base occurs at each position for a set of common SNPs. Tools might use combinatorial functions (for example parsimony) or a likelihood function or model with optimisation such as minimum error correction (MEC) model, expectation-maximisation algorithm (EM), genetic algorithm or Markov chain Monte Carlo (MCMC).
|
|
http://www.w3.org/2000/01/rdf-schema#subClassOf
|
_:180 |
| http://edamontology.org/operation_0282 |
| http://edamontology.org/operation_0283
|
http://edamontology.org/format_3609 |
|
http://www.geneontology.org/formats/oboInOwl#inSubset
|
http://purl.obolibrary.org/obo/edam#formats |
| http://purl.obolibrary.org/obo/edam#edam
|
|
http://www.w3.org/2000/01/rdf-schema#label
|
qualillumina
|
|
http://edamontology.org/created_in
|
1.11
|
|
http://edamontology.org/documentation
|
http://en.wikipedia.org/wiki/Phred_quality_score
|
|
http://www.geneontology.org/formats/oboInOwl#hasDefinition
|
FASTQ format subset for Phred sequencing quality score data only (no sequences) from Illumina 1.5 and before Illumina 1.8.
|
|
http://www.w3.org/1999/02/22-rdf-syntax-ns#type
|
http://www.w3.org/2002/07/owl#Class
|
|
http://www.w3.org/2000/01/rdf-schema#comment
|
Starting in Illumina 1.5 and before Illumina 1.8, the Phred scores 0 to 2 have a slightly different meaning. The values 0 and 1 are no longer used and the value 2, encoded by ASCII 66 "B", is used also at the end of reads as a Read Segment Quality Control Indicator.
|
|
http://www.w3.org/2000/01/rdf-schema#subClassOf
|
http://edamontology.org/format_1931 |
| http://edamontology.org/format_3607
|
http://edamontology.org/operation_3226 |
|
http://www.geneontology.org/formats/oboInOwl#inSubset
|
http://purl.obolibrary.org/obo/edam#edam |
| http://purl.obolibrary.org/obo/edam#operations
|
|
http://www.w3.org/2000/01/rdf-schema#label
|
Variant prioritisation
|
|
http://edamontology.org/created_in
|
1.1
|
|
http://www.geneontology.org/formats/oboInOwl#hasDefinition
|
Identify biologically interesting variants by prioritizing individual variants, for example, homozygous variants absent in control genomes.
|
|
http://www.w3.org/1999/02/22-rdf-syntax-ns#type
|
http://www.w3.org/2002/07/owl#Class
|
|
http://www.w3.org/2000/01/rdf-schema#comment
|
Variant prioritisation can be used for example to produce a list of variants responsible for 'knocking out' genes in specific genomes. Methods amino acid substitution, aggregative approaches, probabilistic approach, inheritance and unified likelihood-frameworks.
|
|
http://www.w3.org/2000/01/rdf-schema#subClassOf
|
http://edamontology.org/operation_3197
|
http://edamontology.org/operation_3227 |
|
http://www.geneontology.org/formats/oboInOwl#inSubset
|
http://purl.obolibrary.org/obo/edam#edam |
| http://purl.obolibrary.org/obo/edam#operations
|
|
http://www.w3.org/2000/01/rdf-schema#label
|
Variant calling
|
|
http://edamontology.org/created_in
|
1.1
|
|
http://www.geneontology.org/formats/oboInOwl#hasNarrowSynonym
|
Exome variant detection |
| Germ line variant calling |
| Somatic variant calling |
| Allele calling |
| Genome variant detection
|
|
http://www.geneontology.org/formats/oboInOwl#hasDefinition
|
Identify and map genomic alterations, including single nucleotide polymorphisms, short indels and structural variants, in a genome sequence.
|
|
http://www.w3.org/1999/02/22-rdf-syntax-ns#type
|
http://www.w3.org/2002/07/owl#Class
|
|
http://www.geneontology.org/formats/oboInOwl#hasExactSynonym
|
Variant mapping
|
|
http://www.w3.org/2000/01/rdf-schema#comment
|
Methods often utilise a database of aligned reads. |
| Variant detection |
| Somatic variant calling is the detection of variations established in somatic cells and hence not inherited as a germ line variant.
|
|
http://www.w3.org/2000/01/rdf-schema#subClassOf
|
http://edamontology.org/operation_3202
|
http://edamontology.org/operation_3228 |
|
http://www.geneontology.org/formats/oboInOwl#inSubset
|
http://purl.obolibrary.org/obo/edam#edam |
| http://purl.obolibrary.org/obo/edam#operations
|
|
http://www.w3.org/2000/01/rdf-schema#label
|
Structural variation detection
|
|
http://edamontology.org/created_in
|
1.1
|
|
http://www.geneontology.org/formats/oboInOwl#hasDefinition
|
Detect large regions in a genome subject to copy-number variation, or other structural variations in genome(s).
|
|
http://www.w3.org/1999/02/22-rdf-syntax-ns#type
|
http://www.w3.org/2002/07/owl#Class
|
|
http://www.geneontology.org/formats/oboInOwl#hasExactSynonym
|
Structural variation discovery
|
|
http://www.w3.org/2000/01/rdf-schema#comment
|
Methods might involve analysis of whole-genome array comparative genome hybridisation or single-nucleotide polymorphism arrays, paired-end mapping of sequencing data, or from analysis of short reads from new sequencing technologies.
|
|
http://www.w3.org/2000/01/rdf-schema#subClassOf
|
http://edamontology.org/operation_3197
|
http://edamontology.org/operation_3222 |
|
http://www.geneontology.org/formats/oboInOwl#inSubset
|
http://purl.obolibrary.org/obo/edam#edam |
| http://purl.obolibrary.org/obo/edam#operations
|
|
http://www.w3.org/2000/01/rdf-schema#label
|
Peak calling
|
|
http://edamontology.org/created_in
|
1.1
|
|
http://www.geneontology.org/formats/oboInOwl#hasNarrowSynonym
|
Peak-pair calling
|
|
http://www.geneontology.org/formats/oboInOwl#hasDefinition
|
Identify putative protein-binding regions in a genome sequence from analysis of Chip-sequencing data or ChIP-on-chip data.
|
|
http://www.w3.org/1999/02/22-rdf-syntax-ns#type
|
http://www.w3.org/2002/07/owl#Class
|
|
http://www.geneontology.org/formats/oboInOwl#hasExactSynonym
|
Protein binding peak detection
|
|
http://www.w3.org/2000/01/rdf-schema#comment
|
Chip-sequencing combines chromatin immunoprecipitation (ChIP) with massively parallel DNA sequencing to generate a set of reads, which are aligned to a genome sequence. The enriched areas contain the binding sites of DNA-associated proteins. For example, a transcription factor binding site. ChIP-on-chip in contrast combines chromatin immunoprecipitation ('ChIP') with microarray ('chip'). "Peak-pair calling" is similar to "Peak calling" in the context of ChIP-exo.
|
|
http://www.w3.org/2000/01/rdf-schema#subClassOf
|
http://edamontology.org/operation_0415
|
http://edamontology.org/operation_3233 |
|
http://www.geneontology.org/formats/oboInOwl#inSubset
|
http://purl.obolibrary.org/obo/edam#edam |
| http://purl.obolibrary.org/obo/edam#operations
|
|
http://www.w3.org/2000/01/rdf-schema#label
|
Copy number estimation
|
|
http://edamontology.org/created_in
|
1.1
|
|
http://www.geneontology.org/formats/oboInOwl#hasDefinition
|
Estimate the number of copies of loci of particular gene(s) in DNA sequences typically from gene-expression profiling technology based on microarray hybridisation-based experiments. For example, estimate copy number (or marker dosage) of a dominant marker in samples from polyploid plant cells or tissues, or chromosomal gains and losses in tumors.
|
|
http://www.w3.org/1999/02/22-rdf-syntax-ns#type
|
http://www.w3.org/2002/07/owl#Class
|
|
http://www.geneontology.org/formats/oboInOwl#hasExactSynonym
|
Transcript copy number estimation
|
|
http://www.w3.org/2000/01/rdf-schema#comment
|
Methods typically implement some statistical model for hypothesis testing, and methods estimate total copy number, i.e. do not distinguish the two inherited chromosomes quantities (specific copy number).
|
|
http://www.w3.org/2000/01/rdf-schema#subClassOf
|
http://edamontology.org/operation_2478
|
http://edamontology.org/format_3686 |
|
http://www.geneontology.org/formats/oboInOwl#inSubset
|
http://purl.obolibrary.org/obo/edam#formats |
| http://purl.obolibrary.org/obo/edam#edam
|
|
http://www.geneontology.org/formats/oboInOwl#hasDbXref
|
http://co.mbine.org/documents/archive
|
|
http://www.w3.org/2000/01/rdf-schema#label
|
COMBINE OMEX
|
|
http://edamontology.org/created_in
|
1.13
|
|
http://edamontology.org/citation
|
http://doi.org/10.1186/s12859-014-0369-z
|
|
http://edamontology.org/documentation
|
http://co.mbine.org/documents/archive
|
|
http://www.geneontology.org/formats/oboInOwl#hasDefinition
|
Open Modeling EXchange format (OMEX) is a ZIPped format for encapsulating all information necessary for a modeling and simulation project in systems biology.
|
|
http://www.w3.org/1999/02/22-rdf-syntax-ns#type
|
http://www.w3.org/2002/07/owl#Class
|
|
http://www.w3.org/2000/01/rdf-schema#comment
|
An OMEX file is a ZIP container that includes a manifest file, listing the content of the archive, an optional metadata file adding information about the archive and its content, and the files describing the model. OMEX is one of the standardised formats within COMBINE (Computational Modeling in Biology Network).
|
|
http://www.w3.org/2000/01/rdf-schema#subClassOf
|
http://edamontology.org/format_2333 |
| http://edamontology.org/format_2013 |
| http://edamontology.org/format_3167
|
http://edamontology.org/format_2352 |
|
http://www.geneontology.org/formats/oboInOwl#hasDbXref
|
http://bioxsd.org |
| http://bioxsd.org/BioXSD-1.1.xsd
|
|
http://www.w3.org/2000/01/rdf-schema#label
|
BioXSD (XML)
|
|
http://edamontology.org/created_in
|
beta12orEarlier
|
|
http://edamontology.org/example
|
http://bioxsd.org/sequenceRecord.xml+json+yaml.xml |
| http://bioxsd.org/accession.xml |
| http://bioxsd.org/exampleFeatureRecords.html |
| http://bioxsd.org/sequenceRecord.xml
|
|
http://edamontology.org/documentation
|
http://bioxsd.org |
| http://bioxsd.org/BioXSD-1.1.xsd
|
|
http://www.geneontology.org/formats/oboInOwl#hasExactSynonym
|
BioXSD in XML format |
| BioXSD+XML |
| BioXSD XML |
| BioXSD in XML |
| BioXSD XML format
|
|
http://edamontology.org/ontology_used
|
Any ontology allowed, none mandatory. Preferrably with URIs but URIs are not mandatory. Non-ontology terms are also allowed as the last resort in case of a lack of suitable ontology.
|
|
http://www.geneontology.org/formats/oboInOwl#inSubset
|
http://purl.obolibrary.org/obo/edam#formats |
| http://purl.obolibrary.org/obo/edam#edam
|
|
http://www.geneontology.org/formats/oboInOwl#comment
|
'BioXSD' belongs to the 'BioXSD|GTrack' ecosystem of generic formats. 'BioXSD in XML' is the XML format based on the common, unified 'BioXSD data model', a.k.a. 'BioXSD|BioJSON|BioYAML'.
|
|
http://edamontology.org/citation
|
http://doi.org/10.7490/f1000research.1113048.1 |
| http://doi.org/10.1186/1471-2105-12-494 |
| http://doi.org/10.1093/bioinformatics/btq391
|
|
http://edamontology.org/repository
|
https://github.com/bioxsd/bioxsd
|
|
http://www.geneontology.org/formats/oboInOwl#hasDefinition
|
BioXSD-schema-based XML format of sequence-based data and some other common data - sequence records, alignments, feature records, references to resources, and more - optimised for integrative bioinformatics, Web services, and object-oriented programming.
|
|
http://www.w3.org/1999/02/22-rdf-syntax-ns#type
|
http://www.w3.org/2002/07/owl#Class
|
|
http://www.w3.org/2000/01/rdf-schema#subClassOf
|
_:192 |
| http://edamontology.org/format_1920 |
| http://edamontology.org/format_1919 |
| _:193 |
| http://edamontology.org/format_2332 |
| http://edamontology.org/format_2555 |
| _:194 |
| http://edamontology.org/format_2571 |
| _:195 |
| _:196
|
|
http://www.geneontology.org/formats/oboInOwl#hasBroadSynonym
|
BioXSD format |
| BioXSD|GTrack |
| BioXSD/GTrack |
| BioXSD|BioJSON|BioYAML |
| BioXSD |
| BioXSD data model
|
http://edamontology.org/data_2018 |
|
http://www.geneontology.org/formats/oboInOwl#inSubset
|
http://purl.obolibrary.org/obo/edam#obsolete
|
|
http://www.w3.org/2002/07/owl#deprecated
|
true
|
|
http://www.w3.org/2000/01/rdf-schema#label
|
Annotation
|
|
http://edamontology.org/created_in
|
beta12orEarlier
|
|
http://www.geneontology.org/formats/oboInOwl#consider
|
http://edamontology.org/data_2048
|
|
http://www.geneontology.org/formats/oboInOwl#hasDefinition
|
A human-readable collection of information which (typically) is generated or collated by hand and which describes a biological entity, phenomena or associated primary (e.g. sequence or structural) data, as distinct from the primary data itself and computer-generated reports derived from it.
|
|
http://www.w3.org/1999/02/22-rdf-syntax-ns#type
|
http://www.w3.org/2002/07/owl#Class
|
|
http://www.w3.org/2000/01/rdf-schema#comment
|
This is a broad data type and is used a placeholder for other, more specific types.
|
|
http://www.w3.org/2000/01/rdf-schema#subClassOf
|
http://www.w3.org/2002/07/owl#DeprecatedClass
|
|
http://edamontology.org/obsolete_since
|
beta13
|
http://edamontology.org/topic_3170 |
|
http://www.geneontology.org/formats/oboInOwl#inSubset
|
http://purl.obolibrary.org/obo/edam#topics
|
|
http://www.w3.org/2000/01/rdf-schema#label
|
RNA-Seq
|
|
http://edamontology.org/created_in
|
1.1
|
|
http://www.geneontology.org/formats/oboInOwl#hasNarrowSynonym
|
miRNA-seq |
| MicroRNA sequencing
|
|
http://www.w3.org/2000/01/rdf-schema#seeAlso
|
https://en.wikipedia.org/wiki/RNA-Seq
|
|
http://www.geneontology.org/formats/oboInOwl#hasDefinition
|
A topic concerning high-throughput sequencing of cDNA to measure the RNA content (transcriptome) of a sample, for example, to investigate how different alleles of a gene are expressed, detect post-transcriptional mutations or identify gene fusions.
|
|
http://www.w3.org/1999/02/22-rdf-syntax-ns#type
|
http://www.w3.org/2002/07/owl#Class
|
|
http://www.geneontology.org/formats/oboInOwl#hasExactSynonym
|
RNA-Seq analysis |
| Small RNA-Seq |
| WTSS |
| Whole transcriptome shotgun sequencing |
| RNA sequencing
|
|
http://www.w3.org/2000/01/rdf-schema#comment
|
This includes small RNA profiling (small RNA-Seq), for example to find novel small RNAs, characterize mutations and analyze expression of small RNAs.
|
|
http://www.w3.org/2000/01/rdf-schema#subClassOf
|
http://edamontology.org/topic_3168
|
|
http://www.geneontology.org/formats/oboInOwl#hasHumanReadableId
|
RNA-Seq
|
http://edamontology.org/topic_3172 |
|
http://www.geneontology.org/formats/oboInOwl#inSubset
|
http://purl.obolibrary.org/obo/edam#events |
| http://purl.obolibrary.org/obo/edam#topics |
| http://purl.obolibrary.org/obo/edam#edam
|
|
http://edamontology.org/isdebtag
|
true
|
|
http://www.w3.org/2000/01/rdf-schema#label
|
Metabolomics
|
|
http://edamontology.org/created_in
|
1.1
|
|
http://www.geneontology.org/formats/oboInOwl#hasNarrowSynonym
|
Mass spectrometry-based metabolomics |
| MS-based metabolomics |
| Metabonomics |
| Metabolites |
| Exometabolomics |
| LC-MS-based metabolomics |
| NMR-based metabolomics |
| Metabolome
|
|
http://www.w3.org/2000/01/rdf-schema#seeAlso
|
https://en.wikipedia.org/wiki/Metabolomics |
| http://purl.bioontology.org/ontology/MSH/D055432
|
|
http://www.geneontology.org/formats/oboInOwl#hasDefinition
|
The systematic study of metabolites, the chemical processes they are involved, and the chemical fingerprints of specific cellular processes in a whole cell, tissue, organ or organism.
|
|
http://www.w3.org/1999/02/22-rdf-syntax-ns#type
|
http://www.w3.org/2002/07/owl#Class
|
|
http://www.w3.org/2000/01/rdf-schema#subClassOf
|
http://edamontology.org/topic_3391
|
|
http://www.geneontology.org/formats/oboInOwl#hasHumanReadableId
|
Metabolomics
|
http://edamontology.org/data_1517 |
|
http://www.geneontology.org/formats/oboInOwl#inSubset
|
http://purl.obolibrary.org/obo/edam#obsolete
|
|
http://www.w3.org/2002/07/owl#deprecated
|
true
|
|
http://www.w3.org/2000/01/rdf-schema#label
|
Restriction enzyme report
|
|
http://edamontology.org/created_in
|
beta12orEarlier
|
|
http://www.geneontology.org/formats/oboInOwl#consider
|
http://edamontology.org/data_0896
|
|
http://www.geneontology.org/formats/oboInOwl#hasDefinition
|
An informative report on a specific restriction enzyme such as enzyme reference data.
|
|
http://www.w3.org/1999/02/22-rdf-syntax-ns#type
|
http://www.w3.org/2002/07/owl#Class
|
|
http://www.w3.org/2000/01/rdf-schema#comment
|
This might include name of enzyme, organism, isoschizomers, methylation, source, suppliers, literature references, or data on restriction enzyme patterns such as name of enzyme, recognition site, length of pattern, number of cuts made by enzyme, details of blunt or sticky end cut etc.
|
|
http://www.w3.org/2000/01/rdf-schema#subClassOf
|
http://www.w3.org/2002/07/owl#DeprecatedClass
|
|
http://edamontology.org/obsolete_since
|
1.5
|
http://edamontology.org/data_1564 |
|
http://www.geneontology.org/formats/oboInOwl#inSubset
|
http://purl.obolibrary.org/obo/edam#obsolete
|
|
http://www.w3.org/2002/07/owl#deprecated
|
true
|
|
http://www.w3.org/2000/01/rdf-schema#label
|
Protein fold recognition report
|
|
http://edamontology.org/created_in
|
beta12orEarlier
|
|
http://www.geneontology.org/formats/oboInOwl#consider
|
http://edamontology.org/data_1277
|
|
http://www.geneontology.org/formats/oboInOwl#hasDefinition
|
A report on known protein structural domains or folds that are recognised (identified) in protein sequence(s).
|
|
http://www.w3.org/1999/02/22-rdf-syntax-ns#type
|
http://www.w3.org/2002/07/owl#Class
|
|
http://www.w3.org/2000/01/rdf-schema#comment
|
Methods use some type of mapping between sequence and fold, for example secondary structure prediction and alignment, profile comparison, sequence properties, homologous sequence search, kernel machines etc. Domains and folds might be taken from SCOP or CATH.
|
|
http://www.w3.org/2000/01/rdf-schema#subClassOf
|
http://www.w3.org/2002/07/owl#DeprecatedClass
|
|
http://edamontology.org/obsolete_since
|
beta12orEarlier
|
http://edamontology.org/operation_3219 |
|
http://www.geneontology.org/formats/oboInOwl#inSubset
|
http://purl.obolibrary.org/obo/edam#edam |
| http://purl.obolibrary.org/obo/edam#operations
|
|
http://www.w3.org/2000/01/rdf-schema#label
|
Read pre-processing
|
|
http://edamontology.org/created_in
|
1.1
|
|
http://www.geneontology.org/formats/oboInOwl#hasDefinition
|
Pre-process sequence reads to ensure (or improve) quality and reliability.
|
|
http://www.w3.org/1999/02/22-rdf-syntax-ns#type
|
http://www.w3.org/2002/07/owl#Class
|
|
http://www.geneontology.org/formats/oboInOwl#hasExactSynonym
|
Sequence read pre-processing
|
|
http://www.w3.org/2000/01/rdf-schema#comment
|
For example process paired end reads to trim low quality ends remove short sequences, identify sequence inserts, detect chimeric reads, or remove low quality sequnces including vector, adaptor, low complexity and contaminant sequences. Sequences might come from genomic DNA library, EST libraries, SSH library and so on.
|
|
http://www.w3.org/2000/01/rdf-schema#subClassOf
|
http://edamontology.org/operation_3218
|
http://edamontology.org/format_3727 |
|
http://www.geneontology.org/formats/oboInOwl#inSubset
|
http://purl.obolibrary.org/obo/edam#formats |
| http://purl.obolibrary.org/obo/edam#edam
|
|
http://www.w3.org/2000/01/rdf-schema#label
|
OME-TIFF
|
|
http://edamontology.org/created_in
|
1.14
|
|
http://www.geneontology.org/formats/oboInOwl#hasDefinition
|
Image file format used by the Open Microscopy Environment (OME).
|
|
http://edamontology.org/documentation
|
http://www.openmicroscopy.org/site/support/ome-model/ome-tiff/specification.html
|
|
http://www.w3.org/1999/02/22-rdf-syntax-ns#type
|
http://www.w3.org/2002/07/owl#Class
|
|
http://www.w3.org/2000/01/rdf-schema#comment
|
An OME-TIFF dataset consists of one or more files in standard TIFF or BigTIFF format, with the file extension .ome.tif or .ome.tiff, and an identical (or in the case of multiple files, nearly identical) string of OME-XML metadata embedded in the ImageDescription tag of each file’s first IFD (Image File Directory). BigTIFF file extensions are also permitted, with the file extension .ome.tf2, .ome.tf8 or .ome.btf, but note these file extensions are an addition to the original specification, and software using an older version of the specification may not be able to handle these file extensions. |
| OME develops open-source software and data format standards for the storage and manipulation of biological microscopy data. It is a joint project between universities, research establishments, industry and the software development community.
|
|
http://www.w3.org/2000/01/rdf-schema#subClassOf
|
http://edamontology.org/format_3547 |
| http://edamontology.org/format_2333
|
http://edamontology.org/format_3728 |
|
http://www.geneontology.org/formats/oboInOwl#inSubset
|
http://purl.obolibrary.org/obo/edam#formats |
| http://purl.obolibrary.org/obo/edam#edam
|
|
http://www.w3.org/2000/01/rdf-schema#label
|
LocARNA PP
|
|
http://edamontology.org/created_in
|
1.14
|
|
http://edamontology.org/documentation
|
http://www.bioinf.uni-freiburg.de/Software/LocARNA/PP/
|
|
http://www.geneontology.org/formats/oboInOwl#hasDefinition
|
The LocARNA PP format combines sequence or alignment information and (respectively, single or consensus) ensemble probabilities into an PP 2.0 record.
|
|
http://www.w3.org/1999/02/22-rdf-syntax-ns#type
|
http://www.w3.org/2002/07/owl#Class
|
|
http://www.w3.org/2000/01/rdf-schema#comment
|
Format for multiple aligned or single sequences together with the probabilistic description of the (consensus) RNA secondary structure ensemble by probabilities of base pairs, base pair stackings, and base pairs and unpaired bases in the loop of base pairs.
|
|
http://www.w3.org/2000/01/rdf-schema#subClassOf
|
http://edamontology.org/format_2330
|
http://edamontology.org/format_3702 |
|
http://www.geneontology.org/formats/oboInOwl#inSubset
|
http://purl.obolibrary.org/obo/edam#formats |
| http://purl.obolibrary.org/obo/edam#edam
|
|
http://www.w3.org/2000/01/rdf-schema#label
|
MSF
|
|
http://edamontology.org/created_in
|
1.14
|
|
http://www.geneontology.org/formats/oboInOwl#hasDefinition
|
Proprietary mass-spectrometry format of Thermo Scientific's ProteomeDiscoverer software.
|
|
http://www.w3.org/1999/02/22-rdf-syntax-ns#type
|
http://www.w3.org/2002/07/owl#Class
|
|
http://www.geneontology.org/formats/oboInOwl#hasExactSynonym
|
Magellan storage file format
|
|
http://www.w3.org/2000/01/rdf-schema#comment
|
This format corresponds to an SQLite database, and you can look into the files with e.g. SQLiteStudio3. There are also some readers (http://doi.org/10.1021/pr2005154) and converters (http://doi.org/10.1016/j.jprot.2015.06.015) for this format available, which re-engineered the database schema, but there is no official DB schema specification of Thermo Scientific for the format.
|
|
http://www.w3.org/2000/01/rdf-schema#subClassOf
|
http://edamontology.org/format_3245
|
http://edamontology.org/topic_0109 |
|
http://www.geneontology.org/formats/oboInOwl#inSubset
|
http://purl.obolibrary.org/obo/edam#obsolete
|
|
http://www.w3.org/2002/07/owl#deprecated
|
true
|
|
http://www.w3.org/2000/01/rdf-schema#label
|
Gene finding
|
|
http://edamontology.org/created_in
|
beta12orEarlier
|
|
http://www.geneontology.org/formats/oboInOwl#consider
|
http://edamontology.org/topic_0114
|
|
http://www.geneontology.org/formats/oboInOwl#hasDefinition
|
Methods that aims to identify, predict, model or analyse genes or gene structure in DNA sequences.
|
|
http://www.w3.org/1999/02/22-rdf-syntax-ns#type
|
http://www.w3.org/2002/07/owl#Class
|
|
http://www.w3.org/2000/01/rdf-schema#comment
|
This includes the study of promoters, coding regions, splice sites, etc. Methods for gene prediction might be ab initio, based on phylogenetic comparisons, use motifs, sequence features, support vector machine, alignment etc.
|
|
http://www.w3.org/2000/01/rdf-schema#subClassOf
|
http://www.w3.org/2002/07/owl#DeprecatedClass
|
|
http://edamontology.org/obsolete_since
|
1.3
|
http://edamontology.org/information_standard |
|
http://www.geneontology.org/formats/oboInOwl#inSubset
|
concept_properties
|
|
http://www.geneontology.org/formats/oboInOwl#comment
|
"Supported by the given data format" here means, that the given format enables representation of data that satisfies the information standard.
|
|
http://www.w3.org/2000/01/rdf-schema#label
|
Information standard
|
|
http://www.geneontology.org/formats/oboInOwl#hasNarrowSynonym
|
Minimum information checklist |
| Minimum information standard
|
|
http://purl.obolibrary.org/obo/is_metadata_tag
|
true
|
|
http://www.geneontology.org/formats/oboInOwl#hasDefinition
|
'Information standard' trailing modifier (qualifier, 'information_standard') of 'xref' links of 'Format' concepts. When 'true', the link is pointing to an information standard supported by the given data format.
|
|
http://www.w3.org/1999/02/22-rdf-syntax-ns#type
|
http://www.w3.org/2002/07/owl#AnnotationProperty
|
http://edamontology.org/topic_0182 |
|
http://www.geneontology.org/formats/oboInOwl#inSubset
|
http://purl.obolibrary.org/obo/edam#obsolete
|
|
http://www.w3.org/2002/07/owl#deprecated
|
true
|
|
http://www.w3.org/2000/01/rdf-schema#label
|
Sequence alignment
|
|
http://edamontology.org/created_in
|
beta12orEarlier
|
|
http://www.geneontology.org/formats/oboInOwl#hasDefinition
|
The alignment of molecular sequences or sequence profiles (representing sequence alignments).
|
|
http://www.w3.org/1999/02/22-rdf-syntax-ns#type
|
http://www.w3.org/2002/07/owl#Class
|
|
http://www.geneontology.org/formats/oboInOwl#replacedBy
|
http://edamontology.org/topic_0080
|
|
http://www.w3.org/2000/01/rdf-schema#comment
|
This includes the generation of alignments (the identification of equivalent sites), the analysis of alignments, editing, visualisation, alignment databases, the alignment (equivalence between sites) of sequence profiles (representing sequence alignments) and so on.
|
|
http://www.w3.org/2000/01/rdf-schema#subClassOf
|
http://www.w3.org/2002/07/owl#DeprecatedClass
|
|
http://edamontology.org/obsolete_since
|
1.7
|
http://edamontology.org/format_3772 |
|
http://www.geneontology.org/formats/oboInOwl#hasDbXref
|
http://bioxsd.org
|
|
http://www.w3.org/2000/01/rdf-schema#label
|
BioJSON (BioXSD)
|
|
http://edamontology.org/created_in
|
1.16
|
|
http://edamontology.org/example
|
http://bioxsd.org/sequenceRecord.xml+json+yaml.xml |
| http://bioxsd.org/sequenceRecord.json
|
|
http://edamontology.org/documentation
|
http://bioxsd.org
|
|
http://www.geneontology.org/formats/oboInOwl#hasExactSynonym
|
BioXSD BioJSON format |
| BioJSON (BioXSD data model) |
| BioXSD BioJSON |
| BioXSD JSON format |
| BioXSD|BioJSON|BioYAML BioJSON |
| BioXSD+JSON |
| BioXSD JSON |
| BioXSD in JSON format |
| BioXSD in JSON |
| BioXSD|GTrack BioJSON |
| BioXSD/GTrack BioJSON |
| BioJSON format (BioXSD)
|
|
http://www.geneontology.org/formats/oboInOwl#inSubset
|
http://purl.obolibrary.org/obo/edam#formats |
| http://purl.obolibrary.org/obo/edam#edam
|
|
http://www.geneontology.org/formats/oboInOwl#comment
|
Work in progress. 'BioXSD' belongs to the 'BioXSD|GTrack' ecosystem of generic formats. 'BioJSON' is the JSON format based on the common, unified 'BioXSD data model', a.k.a. 'BioXSD|BioJSON|BioYAML'.
|
|
http://edamontology.org/citation
|
http://doi.org/10.7490/f1000research.1113048.1
|
|
http://edamontology.org/repository
|
https://github.com/bioxsd/bioxsd
|
|
http://www.geneontology.org/formats/oboInOwl#hasDefinition
|
BioJSON is a BioXSD-schema-based JSON format of sequence-based data and some other common data - sequence records, alignments, feature records, references to resources, and more - optimised for integrative bioinformatics, web applications and APIs, and object-oriented programming.
|
|
http://www.w3.org/1999/02/22-rdf-syntax-ns#type
|
http://www.w3.org/2002/07/owl#Class
|
|
http://www.w3.org/2000/01/rdf-schema#subClassOf
|
http://edamontology.org/format_1920 |
| _:208 |
| http://edamontology.org/format_1921 |
| http://edamontology.org/format_1919 |
| _:209 |
| http://edamontology.org/format_2571 |
| _:210 |
| http://edamontology.org/format_3464 |
| _:211 |
| _:212
|
http://edamontology.org/format_3773 |
|
http://www.geneontology.org/formats/oboInOwl#hasDbXref
|
http://bioxsd.org
|
|
http://www.w3.org/2000/01/rdf-schema#label
|
BioYAML
|
|
http://edamontology.org/created_in
|
1.16
|
|
http://edamontology.org/example
|
http://bioxsd.org/sequenceRecord.xml+json+yaml.xml |
| http://bioxsd.org/sequenceRecord.yaml
|
|
http://edamontology.org/documentation
|
http://bioxsd.org
|
|
http://www.geneontology.org/formats/oboInOwl#hasExactSynonym
|
BioXSD|BioJSON|BioYAML BioYAML |
| BioXSD BioYAML |
| BioXSD+YAML |
| BioXSD YAML format |
| BioXSD/GTrack BioYAML |
| BioXSD in YAML format |
| BioXSD BioYAML format |
| BioXSD YAML |
| BioXSD in YAML |
| BioYAML (BioXSD) |
| BioYAML format (BioXSD) |
| BioYAML format |
| BioYAML (BioXSD data model) |
| BioXSD|GTrack BioYAML
|
|
http://www.geneontology.org/formats/oboInOwl#inSubset
|
http://purl.obolibrary.org/obo/edam#formats |
| http://purl.obolibrary.org/obo/edam#edam
|
|
http://www.geneontology.org/formats/oboInOwl#comment
|
Work in progress. 'BioXSD' belongs to the 'BioXSD|GTrack' ecosystem of generic formats. 'BioYAML' is the YAML format based on the common, unified 'BioXSD data model', a.k.a. 'BioXSD|BioJSON|BioYAML'.
|
|
http://edamontology.org/citation
|
http://doi.org/10.7490/f1000research.1113048.1
|
|
http://edamontology.org/repository
|
https://github.com/bioxsd/bioxsd
|
|
http://www.geneontology.org/formats/oboInOwl#hasDefinition
|
BioYAML is a BioXSD-schema-based YAML format of sequence-based data and some other common data - sequence records, alignments, feature records, references to resources, and more - optimised for integrative bioinformatics, web APIs, human readability and editting, and object-oriented programming.
|
|
http://www.w3.org/1999/02/22-rdf-syntax-ns#type
|
http://www.w3.org/2002/07/owl#Class
|
|
http://www.w3.org/2000/01/rdf-schema#subClassOf
|
http://edamontology.org/format_1920 |
| http://edamontology.org/format_1921 |
| http://edamontology.org/format_1919 |
| _:219 |
| _:220 |
| http://edamontology.org/format_2571 |
| _:221 |
| http://edamontology.org/format_3750 |
| _:222 |
| _:223
|
http://edamontology.org/format_3776 |
|
http://www.geneontology.org/formats/oboInOwl#inSubset
|
http://purl.obolibrary.org/obo/edam#formats |
| http://purl.obolibrary.org/obo/edam#edam
|
|
http://www.geneontology.org/formats/oboInOwl#comment
|
'BTrack' belongs to the 'BioXSD|GTrack' ecosystem of generic formats, and particular to its subset, the 'GTrack ecosystem' (GTrack, GSuite, BTrack). 'BTrack' is the binary, optionally compressed HDF5-based version of the GTrack and GSuite formats.
|
|
http://www.w3.org/2000/01/rdf-schema#label
|
BTrack
|
|
http://edamontology.org/created_in
|
1.16
|
|
http://edamontology.org/repository
|
https://github.com/gtrack/gtrack
|
|
http://www.geneontology.org/formats/oboInOwl#hasDefinition
|
BTrack is an HDF5-based binary format for genome or sequence feature tracks and their collections, suitable for integrative multi-track analysis. BTrack is a binary, compressed alternative to the GTrack and GSuite formats.
|
|
http://www.w3.org/1999/02/22-rdf-syntax-ns#type
|
http://www.w3.org/2002/07/owl#Class
|
|
http://www.geneontology.org/formats/oboInOwl#hasExactSynonym
|
GTrack|GSuite|BTrack BTrack |
| GTrack|BTrack|GSuite BTrack |
| BTrack format |
| BioXSD|GTrack BTrack |
| BioXSD/GTrack BTrack |
| BTrack (GTrack ecosystem of formats)
|
|
http://www.w3.org/2000/01/rdf-schema#subClassOf
|
http://edamontology.org/format_1920 |
| http://edamontology.org/format_2548 |
| http://edamontology.org/format_2333 |
| http://edamontology.org/format_2919
|
http://edamontology.org/format_3775 |
|
http://www.geneontology.org/formats/oboInOwl#hasDbXref
|
https://hyperbrowser.uio.no/gsuite/static/hyperbrowser/gsuite/GSuite_specification.html |
| https://hyperbrowser.uio.no/gsuite/static/hyperbrowser/gsuite/GSuite_specification.txt
|
|
http://www.w3.org/2000/01/rdf-schema#label
|
GSuite
|
|
http://edamontology.org/created_in
|
1.16
|
|
http://edamontology.org/example
|
https://github.com/gtrack/gtrack/tree/master/gsuite/examples
|
|
http://edamontology.org/documentation
|
https://hyperbrowser.uio.no/gsuite/static/hyperbrowser/gsuite/GSuite_specification.txt |
| https://hyperbrowser.uio.no/gsuite/static/hyperbrowser/gsuite/GSuite_specification.html
|
|
http://www.geneontology.org/formats/oboInOwl#hasExactSynonym
|
GSuite format |
| GTrack|BTrack|GSuite GSuite |
| GTrack|GSuite|BTrack GSuite |
| GSuite (GTrack ecosystem of formats) |
| BioXSD|GTrack GSuite |
| BioXSD/GTrack GSuite
|
|
http://www.geneontology.org/formats/oboInOwl#inSubset
|
http://purl.obolibrary.org/obo/edam#formats |
| http://purl.obolibrary.org/obo/edam#edam
|
|
http://www.geneontology.org/formats/oboInOwl#comment
|
'GSuite' belongs to the 'BioXSD|GTrack' ecosystem of generic formats, and particular to its subset, the 'GTrack ecosystem' (GTrack, GSuite, BTrack). 'GSuite' is the tabular format for an annotated collection of individual GTrack files.
|
|
http://edamontology.org/citation
|
http://doi.org/10.7490/f1000research.1112716.1 |
| http://dx.doi.org/10.1101/067561
|
|
http://edamontology.org/repository
|
https://github.com/gtrack/gtrack
|
|
http://www.w3.org/2000/01/rdf-schema#seeAlso
|
https://hyperbrowser.uio.no/gsuite
|
|
http://www.geneontology.org/formats/oboInOwl#hasDefinition
|
GSuite is a tabular format for collections of genome or sequence feature tracks, suitable for integrative multi-track analysis. GSuite contains links to genome/sequence tracks, with additional metadata.
|
|
http://www.w3.org/1999/02/22-rdf-syntax-ns#type
|
http://www.w3.org/2002/07/owl#Class
|
|
http://www.w3.org/2000/01/rdf-schema#subClassOf
|
http://edamontology.org/format_1920 |
| http://edamontology.org/format_2330
|
http://edamontology.org/format_3747 |
|
http://www.geneontology.org/formats/oboInOwl#inSubset
|
http://purl.obolibrary.org/obo/edam#formats |
| http://purl.obolibrary.org/obo/edam#edam
|
|
http://www.geneontology.org/formats/oboInOwl#hasDbXref
|
http://purl.obolibrary.org/obo/MS_1001422
|
|
http://www.w3.org/2000/01/rdf-schema#label
|
protXML
|
|
http://edamontology.org/created_in
|
1.15
|
|
http://www.w3.org/2000/01/rdf-schema#seeAlso
|
http://doi.org/10.1038/msb4100024 |
| http://sashimi.sourceforge.net/schema_revision/protXML/protXML_v3.xsd
|
|
http://edamontology.org/documentation
|
http://tools.proteomecenter.org/formats/protXML/protXML_xmlspy_docs.html
|
|
http://www.geneontology.org/formats/oboInOwl#hasDefinition
|
A format for storage, exchange, and processing of protein identifications created from ms/ms-derived peptide sequence data.
|
|
http://www.w3.org/1999/02/22-rdf-syntax-ns#type
|
http://www.w3.org/2002/07/owl#Class
|
|
http://www.w3.org/2000/01/rdf-schema#comment
|
No human-consumable information about this format is available (see http://tools.proteomecenter.org/wiki/index.php?title=Formats:protXML).
|
|
http://www.w3.org/2000/01/rdf-schema#subClassOf
|
http://edamontology.org/format_2332 |
| http://edamontology.org/format_3245
|
http://edamontology.org/format_3746 |
|
http://www.geneontology.org/formats/oboInOwl#inSubset
|
http://purl.obolibrary.org/obo/edam#formats |
| http://purl.obolibrary.org/obo/edam#edam
|
|
http://www.w3.org/2000/01/rdf-schema#label
|
BIOM format
|
|
http://edamontology.org/file_extension
|
biom
|
|
http://edamontology.org/created_in
|
1.15
|
|
http://edamontology.org/citation
|
http://doi.org/10.1186/2047-217X-1-7
|
|
http://www.geneontology.org/formats/oboInOwl#hasDefinition
|
The BIological Observation Matrix (BIOM) is a format for representing biological sample by observation contingency tables in broad areas of comparative omics. The primary use of this format is to represent OTU tables and metagenome tables.
|
|
http://edamontology.org/documentation
|
http://biom-format.org
|
|
http://www.w3.org/1999/02/22-rdf-syntax-ns#type
|
http://www.w3.org/2002/07/owl#Class
|
|
http://www.geneontology.org/formats/oboInOwl#hasExactSynonym
|
BIological Observation Matrix format
|
|
http://www.w3.org/2000/01/rdf-schema#comment
|
BIOM is a recognised standard for the Earth Microbiome Project, and is a project supported by Genomics Standards Consortium. Supported in QIIME, Mothur, MEGAN, etc.
|
|
http://www.w3.org/2000/01/rdf-schema#subClassOf
|
http://edamontology.org/format_2330 |
| http://edamontology.org/format_3706
|
http://edamontology.org/operation_2871 |
|
http://www.geneontology.org/formats/oboInOwl#inSubset
|
http://purl.obolibrary.org/obo/edam#edam |
| http://purl.obolibrary.org/obo/edam#operations
|
|
http://www.w3.org/2000/01/rdf-schema#label
|
Sequence tagged site (STS) mapping
|
|
http://edamontology.org/created_in
|
beta12orEarlier
|
|
http://www.geneontology.org/formats/oboInOwl#hasDefinition
|
Generate a physical DNA map (sequence map) from analysis of sequence tagged sites (STS).
|
|
http://www.w3.org/1999/02/22-rdf-syntax-ns#type
|
http://www.w3.org/2002/07/owl#Class
|
|
http://www.geneontology.org/formats/oboInOwl#hasExactSynonym
|
Sequence mapping
|
|
http://www.w3.org/2000/01/rdf-schema#comment
|
An STS is a short subsequence of known sequence and location that occurs only once in the chromosome or genome that is being mapped. Sources of STSs include 1. expressed sequence tags (ESTs), simple sequence length polymorphisms (SSLPs), and random genomic sequences from cloned genomic DNA or database sequences.
|
|
http://www.w3.org/2000/01/rdf-schema#subClassOf
|
http://edamontology.org/operation_2944 |
| _:226
|
http://edamontology.org/data_1415 |
|
http://www.geneontology.org/formats/oboInOwl#inSubset
|
http://purl.obolibrary.org/obo/edam#obsolete
|
|
http://www.w3.org/2002/07/owl#deprecated
|
true
|
|
http://www.w3.org/2000/01/rdf-schema#label
|
Sequence alignment report (site conservation)
|
|
http://edamontology.org/created_in
|
beta12orEarlier
|
|
http://www.geneontology.org/formats/oboInOwl#hasDefinition
|
Data on character conservation in a molecular sequence alignment.
|
|
http://www.geneontology.org/formats/oboInOwl#consider
|
http://edamontology.org/data_2161
|
|
http://www.w3.org/1999/02/22-rdf-syntax-ns#type
|
http://www.w3.org/2002/07/owl#Class
|
|
http://www.w3.org/2000/01/rdf-schema#comment
|
This is a broad data type and is used a placeholder for other, more specific types. It is primarily intended to help navigation of EDAM and would not typically be used for annotation. Use this concept for calculated substitution rates, relative site variability, data on sites with biased properties, highly conserved or very poorly conserved sites, regions, blocks etc.
|
|
http://www.w3.org/2000/01/rdf-schema#subClassOf
|
http://www.w3.org/2002/07/owl#DeprecatedClass
|
|
http://edamontology.org/obsolete_since
|
1.4
|
http://edamontology.org/topic_2819 |
|
http://www.geneontology.org/formats/oboInOwl#inSubset
|
http://purl.obolibrary.org/obo/edam#obsolete
|
|
http://www.w3.org/2002/07/owl#deprecated
|
true
|
|
http://www.w3.org/2000/01/rdf-schema#label
|
Invertebrates
|
|
http://edamontology.org/created_in
|
beta12orEarlier
|
|
http://www.geneontology.org/formats/oboInOwl#hasDefinition
|
Invertebrates, e.g. information on a specific invertebrate genome including molecular sequences, genes and annotation.
|
|
http://edamontology.org/deprecation_comment
|
(jison)Out of EDAM scope. While very useful to have a basic set of IDs for organisms, should find a better way to provide this e.g. in bio.tools (NCBI taxon ID subset).
|
|
http://www.geneontology.org/formats/oboInOwl#consider
|
http://edamontology.org/topic_0621
|
|
http://www.w3.org/1999/02/22-rdf-syntax-ns#type
|
http://www.w3.org/2002/07/owl#Class
|
|
http://www.w3.org/2000/01/rdf-schema#comment
|
The resource may be specific to an invertebrate, a group of invertebrates or all invertebrates.
|
|
http://www.w3.org/2000/01/rdf-schema#subClassOf
|
http://www.w3.org/2002/07/owl#DeprecatedClass
|
|
http://edamontology.org/oldParent
|
http://edamontology.org/topic_3500
|
|
http://edamontology.org/obsolete_since
|
1.17
|
http://edamontology.org/topic_2821 |
|
http://www.geneontology.org/formats/oboInOwl#inSubset
|
http://purl.obolibrary.org/obo/edam#obsolete
|
|
http://www.w3.org/2002/07/owl#deprecated
|
true
|
|
http://www.w3.org/2000/01/rdf-schema#label
|
Unicellular eukaryotes
|
|
http://edamontology.org/created_in
|
beta12orEarlier
|
|
http://edamontology.org/deprecation_comment
|
(jison)Out of EDAM scope. While very useful to have a basic set of IDs for organisms, should find a better way to provide this e.g. in bio.tools (NCBI taxon ID subset).
|
|
http://www.geneontology.org/formats/oboInOwl#hasDefinition
|
Unicellular eukaryotes, e.g. information on a unicellular eukaryote genome including molecular sequences, genes and annotation.
|
|
http://www.geneontology.org/formats/oboInOwl#consider
|
http://edamontology.org/topic_0621
|
|
http://www.w3.org/1999/02/22-rdf-syntax-ns#type
|
http://www.w3.org/2002/07/owl#Class
|
|
http://www.w3.org/2000/01/rdf-schema#comment
|
The resource may be specific to a unicellular eukaryote, a group of unicellular eukaryotes or all unicellular eukaryotes.
|
|
http://www.w3.org/2000/01/rdf-schema#subClassOf
|
http://www.w3.org/2002/07/owl#DeprecatedClass
|
|
http://edamontology.org/oldParent
|
http://edamontology.org/topic_2818
|
|
http://edamontology.org/obsolete_since
|
1.17
|
http://edamontology.org/operation_0245 |
|
http://www.geneontology.org/formats/oboInOwl#inSubset
|
http://purl.obolibrary.org/obo/edam#edam |
| http://purl.obolibrary.org/obo/edam#operations
|
|
http://www.w3.org/2000/01/rdf-schema#label
|
Protein structural motif recognition
|
|
http://edamontology.org/created_in
|
beta12orEarlier
|
|
http://www.geneontology.org/formats/oboInOwl#hasDefinition
|
Identify or screen for 3D structural motifs in protein structure(s).
|
|
http://www.w3.org/1999/02/22-rdf-syntax-ns#type
|
http://www.w3.org/2002/07/owl#Class
|
|
http://www.geneontology.org/formats/oboInOwl#hasExactSynonym
|
Protein structural feature identification
|
|
http://www.w3.org/2000/01/rdf-schema#comment
|
This includes conserved substructures and conserved geometry, such as spatial arrangement of secondary structure or protein backbone. Methods might use structure alignment, structural templates, searches for similar electrostatic potential and molecular surface shape, surface-mapping of phylogenetic information etc.
|
|
http://www.w3.org/2000/01/rdf-schema#subClassOf
|
http://edamontology.org/operation_2406 |
| _:242 |
| http://edamontology.org/operation_3092
|
http://edamontology.org |
|
http://purl.obolibrary.org/obo/remark
|
EDAM editors: Jon Ison, Matúš Kalaš, Hervé Ménager, and Veit Schwämmle. Contributors: see http://edamontologydocs.readthedocs.io/en/latest/contributors.html. License: see http://edamontologydocs.readthedocs.io/en/latest/license.html. |
| EDAM is an ontology of well established, familiar concepts that are prevalent within bioinformatics, including types of data and data identifiers, data formats, operations and topics. EDAM is a simple ontology - essentially a set of terms with synonyms and definitions - organised into an intuitive hierarchy for convenient use by curators, software developers and end-users. EDAM is suitable for large-scale semantic annotations and categorisation of diverse bioinformatics resources. EDAM is also suitable for diverse application including for example within workbenches and workflow-management systems, software distributions, and resource registries.
|
|
http://edamontology.org/next_id
|
3918
|
|
http://purl.obolibrary.org/obo/idspace
|
EDAM http://edamontology.org/ "EDAM relations and concept properties" |
| EDAM_format http://edamontology.org/format_ "EDAM data formats" |
| EDAM_topic http://edamontology.org/topic_ "EDAM topics" |
| EDAM_operation http://edamontology.org/operation_ "EDAM operations" |
| EDAM_data http://edamontology.org/data_ "EDAM types of data"
|
|
http://xmlns.com/foaf/0.1/page
|
http://edamontology.org/page
|
|
http://purl.org/dc/elements/1.1/creator
|
Hervé Ménager |
| Jon Ison |
| Matúš Kalaš
|
|
http://purl.org/dc/elements/1.1/format
|
application/rdf+xml
|
|
http://purl.obolibrary.org/obo/date
|
16.07.2019 19:43 UTC
|
|
http://www.geneontology.org/formats/oboInOwl#savedBy
|
Jon Ison, Matúš Kalaš, Hervé Ménager
|
|
http://purl.obolibrary.org/obo/default-relationship-id-prefix
|
EDAM
|
|
http://usefulinc.com/ns/doap#Version
|
1.23
|
|
http://www.w3.org/2000/01/rdf-schema#isDefinedBy
|
http://edamontology.org/EDAM.owl
|
|
http://www.w3.org/1999/02/22-rdf-syntax-ns#type
|
http://www.w3.org/2002/07/owl#Ontology
|
|
http://www.geneontology.org/formats/oboInOwl#hasSubset
|
identifiers "EDAM types of identifiers" |
| relations "EDAM relations" |
| edam "EDAM" |
| concept_properties "EDAM concept properties" |
| data "EDAM types of data" |
| topics "EDAM topics" |
| operations "EDAM operations" |
| formats "EDAM data formats"
|
|
http://purl.org/dc/elements/1.1/contributor
|
Veit Schwämmle
|
|
http://purl.org/dc/elements/1.1/title
|
Bioinformatics operations, data types, formats, identifiers and topics
|
http://edamontology.org/operation_0281 |
|
http://www.geneontology.org/formats/oboInOwl#inSubset
|
http://purl.obolibrary.org/obo/edam#obsolete
|
|
http://www.w3.org/2002/07/owl#deprecated
|
true
|
|
http://www.w3.org/2000/01/rdf-schema#label
|
Genetic marker identification
|
|
http://edamontology.org/created_in
|
beta12orEarlier
|
|
http://www.geneontology.org/formats/oboInOwl#consider
|
http://edamontology.org/operation_0415
|
|
http://www.geneontology.org/formats/oboInOwl#hasDefinition
|
Identify genetic markers in DNA sequences.
|
|
http://www.w3.org/1999/02/22-rdf-syntax-ns#type
|
http://www.w3.org/2002/07/owl#Class
|
|
http://www.w3.org/2000/01/rdf-schema#comment
|
A genetic marker is any DNA sequence of known chromosomal location that is associated with and specific to a particular gene or trait. This includes short sequences surrounding a SNP, Sequence-Tagged Sites (STS) which are well suited for PCR amplification, a longer minisatellites sequence etc.
|
|
http://www.w3.org/2000/01/rdf-schema#subClassOf
|
http://www.w3.org/2002/07/owl#DeprecatedClass
|
|
http://edamontology.org/obsolete_since
|
beta13
|
http://edamontology.org/data_3128 |
|
http://www.geneontology.org/formats/oboInOwl#inSubset
|
http://purl.obolibrary.org/obo/edam#edam |
| http://purl.obolibrary.org/obo/edam#data
|
|
http://www.geneontology.org/formats/oboInOwl#comment
|
The report may be based on analysis of nucleic acid sequence or structural data, or any annotation or information about specific nucleic acid 3D structure(s) or such structures in general.
|
|
http://www.w3.org/2000/01/rdf-schema#label
|
Nucleic acid structure report
|
|
http://edamontology.org/created_in
|
beta13
|
|
http://www.geneontology.org/formats/oboInOwl#hasNarrowSynonym
|
Quadruplexes (report) |
| Stem loop (report) |
| d-loop (report)
|
|
http://www.geneontology.org/formats/oboInOwl#hasDefinition
|
A human-readable collection of information about regions within a nucleic acid sequence which form secondary or tertiary (3D) structures.
|
|
http://www.w3.org/1999/02/22-rdf-syntax-ns#type
|
http://www.w3.org/2002/07/owl#Class
|
|
http://www.geneontology.org/formats/oboInOwl#hasExactSynonym
|
Nucleic acid features (structure)
|
|
http://www.w3.org/2000/01/rdf-schema#subClassOf
|
http://edamontology.org/data_2084 |
| http://edamontology.org/data_2085
|
http://edamontology.org/has_output |
|
http://purl.obolibrary.org/obo/is_anti_symmetric
|
false
|
|
http://www.w3.org/2000/01/rdf-schema#label
|
has output
|
|
http://purl.obolibrary.org/obo/is_reflexive
|
false
|
|
http://www.geneontology.org/formats/oboInOwl#isCyclic
|
true
|
|
http://www.geneontology.org/formats/oboInOwl#inSubset
|
edam |
| relations
|
|
http://www.w3.org/2000/01/rdf-schema#range
|
http://edamontology.org/data_0006
|
|
http://purl.obolibrary.org/obo/is_symmetric
|
false
|
|
http://www.w3.org/2000/01/rdf-schema#domain
|
http://edamontology.org/operation_0004
|
|
http://www.w3.org/2002/07/owl#inverseOf
|
http://edamontology.org/is_output_of
|
|
http://www.w3.org/2000/01/rdf-schema#seeAlso
|
http://wsio.org/has_output |
| "http://purl.obolibrary.org/obo/OBI_0000299"
|
|
http://www.geneontology.org/formats/oboInOwl#hasDefinition
|
'A has_output B' defines for the subject A, that it has the object B as a necessary or actual output or output argument.
|
|
http://www.w3.org/1999/02/22-rdf-syntax-ns#type
|
http://www.w3.org/2002/07/owl#ObjectProperty
|
|
http://www.w3.org/2000/01/rdf-schema#comment
|
Subject A can either be concept that is or has an 'Operation' function, or an entity outside of an ontology (or an ontology concept in a role of an entity being semantically annotated) that has an 'Operation' function or is an 'Operation'. Object B can be any concept or entity. In EDAM, only 'has_output' is explicitly defined between EDAM concepts ('Operation' 'has_output' 'Data'). The inverse, 'is_output_of', is not explicitly defined.
|
|
http://purl.obolibrary.org/obo/transitive_over
|
OBO_REL:is_a
|
|
http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym
|
OBO_REL:has_participant
|
http://edamontology.org/data_3148 |
|
http://www.geneontology.org/formats/oboInOwl#inSubset
|
http://purl.obolibrary.org/obo/edam#edam |
| http://purl.obolibrary.org/obo/edam#data
|
|
http://www.w3.org/2000/01/rdf-schema#label
|
Gene family report
|
|
http://edamontology.org/created_in
|
beta13
|
|
http://www.geneontology.org/formats/oboInOwl#hasDefinition
|
A human-readable collection of information about a particular family of genes, typically a set of genes with similar sequence that originate from duplication of a common ancestor gene, or any other classification of nucleic acid sequences or structures that reflects gene structure.
|
|
http://www.w3.org/1999/02/22-rdf-syntax-ns#type
|
http://www.w3.org/2002/07/owl#Class
|
|
http://www.geneontology.org/formats/oboInOwl#hasExactSynonym
|
Gene annotation (homology information) |
| Gene family annotation |
| Gene homology (report) |
| Gene annotation (homology) |
| Homology information
|
|
http://www.w3.org/2000/01/rdf-schema#comment
|
This includes reports on on gene homologues between species.
|
|
http://www.w3.org/2000/01/rdf-schema#subClassOf
|
http://edamontology.org/data_2084
|
|
http://www.geneontology.org/formats/oboInOwl#hasBroadSynonym
|
Nucleic acid classification
|
http://edamontology.org/data_3134 |
|
http://www.geneontology.org/formats/oboInOwl#inSubset
|
http://purl.obolibrary.org/obo/edam#edam |
| http://purl.obolibrary.org/obo/edam#data
|
|
http://www.w3.org/2000/01/rdf-schema#label
|
Gene transcript report
|
|
http://edamontology.org/created_in
|
beta13
|
|
http://www.geneontology.org/formats/oboInOwl#hasDefinition
|
An informative report on features of a messenger RNA (mRNA) molecules including precursor RNA, primary (unprocessed) transcript and fully processed molecules. This includes reports on a specific gene transcript, clone or EST.
|
|
http://www.w3.org/1999/02/22-rdf-syntax-ns#type
|
http://www.w3.org/2002/07/owl#Class
|
|
http://www.geneontology.org/formats/oboInOwl#hasExactSynonym
|
Transcript (report) |
| Gene transcript annotation |
| mRNA features |
| mRNA (report) |
| Nucleic acid features (mRNA features) |
| Clone or EST (report)
|
|
http://www.w3.org/2000/01/rdf-schema#comment
|
This includes 5'untranslated region (5'UTR), coding sequences (CDS), exons, intervening sequences (intron) and 3'untranslated regions (3'UTR).
|
|
http://www.w3.org/2000/01/rdf-schema#subClassOf
|
http://edamontology.org/data_1276
|
http://edamontology.org/data_0912 |
|
http://www.geneontology.org/formats/oboInOwl#inSubset
|
http://purl.obolibrary.org/obo/edam#edam |
| http://purl.obolibrary.org/obo/edam#data
|
|
http://www.geneontology.org/formats/oboInOwl#comment
|
Nucleic acid structural properties stiffness, curvature, twist/roll data or other conformational parameters or properties.
|
|
http://www.w3.org/2000/01/rdf-schema#label
|
Nucleic acid property
|
|
http://edamontology.org/created_in
|
beta12orEarlier
|
|
http://www.geneontology.org/formats/oboInOwl#hasNarrowSynonym
|
Nucleic acid structural property |
| GC-content |
| Nucleic acid property (structural)
|
|
http://www.geneontology.org/formats/oboInOwl#hasDefinition
|
A report of primarily non-positional data describing intrinsic physical, chemical or other properties of a nucleic acid molecule.
|
|
http://www.w3.org/1999/02/22-rdf-syntax-ns#type
|
http://www.w3.org/2002/07/owl#Class
|
|
http://www.geneontology.org/formats/oboInOwl#hasExactSynonym
|
Nucleic acid physicochemical property
|
|
http://www.w3.org/2000/01/rdf-schema#comment
|
This is a broad data type and is used a placeholder for other, more specific types.
|
|
http://www.w3.org/2000/01/rdf-schema#subClassOf
|
http://edamontology.org/data_2087
|
http://edamontology.org/topic_0659 |
|
http://www.geneontology.org/formats/oboInOwl#inSubset
|
http://purl.obolibrary.org/obo/edam#topics |
| http://purl.obolibrary.org/obo/edam#edam
|
|
http://edamontology.org/isdebtag
|
true
|
|
http://www.w3.org/2000/01/rdf-schema#label
|
Functional, regulatory and non-coding RNA
|
|
http://edamontology.org/created_in
|
beta12orEarlier
|
|
http://www.geneontology.org/formats/oboInOwl#hasNarrowSynonym
|
piRNA |
| snoRNA |
| Small non-coding RNA |
| piwi-interacting RNA |
| Small nuclear RNA |
| ncRNA |
| Small nucleolar RNA |
| Functional RNA |
| Long ncRNA |
| Lon non-coding RNA |
| Small ncRNA |
| Regulatory RNA |
| Non-coding RNA |
| snRNA |
| lncRNA |
| siRNA |
| Small interfering RNA |
| microRNA |
| miRNA
|
|
http://www.w3.org/2000/01/rdf-schema#seeAlso
|
https://en.wikipedia.org/wiki/Non-coding_RNA
|
|
http://www.geneontology.org/formats/oboInOwl#hasDefinition
|
Non-coding or functional RNA sequences, including regulatory RNA sequences, ribosomal RNA (rRNA) and transfer RNA (tRNA).
|
|
http://www.w3.org/1999/02/22-rdf-syntax-ns#type
|
http://www.w3.org/2002/07/owl#Class
|
|
http://www.w3.org/2000/01/rdf-schema#comment
|
Non-coding RNA includes piwi-interacting RNA (piRNA), small nuclear RNA (snRNA) and small nucleolar RNA (snoRNA). Regulatory RNA includes microRNA (miRNA) - short single stranded RNA molecules that regulate gene expression, and small interfering RNA (siRNA).
|
|
http://www.w3.org/2000/01/rdf-schema#subClassOf
|
http://edamontology.org/topic_0099 |
| http://edamontology.org/topic_0114
|
|
http://www.geneontology.org/formats/oboInOwl#hasHumanReadableId
|
Functional_regulatory_and_non-coding_RNA
|
http://edamontology.org/data_0916 |
|
http://www.geneontology.org/formats/oboInOwl#inSubset
|
http://purl.obolibrary.org/obo/edam#edam |
| http://purl.obolibrary.org/obo/edam#data
|
|
http://www.geneontology.org/formats/oboInOwl#hasDbXref
|
Moby:GeneInfo |
| Moby:gene |
| Moby_namespace:Human_Readable_Description
|
|
http://www.w3.org/2000/01/rdf-schema#label
|
Gene report
|
|
http://edamontology.org/created_in
|
beta12orEarlier
|
|
http://www.geneontology.org/formats/oboInOwl#hasDefinition
|
A report on predicted or actual gene structure, regions which make an RNA product and features such as promoters, coding regions, splice sites etc.
|
|
http://www.w3.org/1999/02/22-rdf-syntax-ns#type
|
http://www.w3.org/2002/07/owl#Class
|
|
http://www.geneontology.org/formats/oboInOwl#hasExactSynonym
|
Gene and transcript structure (report) |
| Nucleic acid features (gene and transcript structure) |
| Gene structure (repot) |
| Gene annotation |
| Gene function (report) |
| Gene features report
|
|
http://www.w3.org/2000/01/rdf-schema#comment
|
This includes any report on a particular locus or gene. This might include the gene name, description, summary and so on. It can include details about the function of a gene, such as its encoded protein or a functional classification of the gene sequence along according to the encoded protein(s).
|
|
http://www.w3.org/2000/01/rdf-schema#subClassOf
|
http://edamontology.org/data_2084
|
http://edamontology.org/data_0906 |
|
http://www.geneontology.org/formats/oboInOwl#inSubset
|
http://purl.obolibrary.org/obo/edam#edam |
| http://purl.obolibrary.org/obo/edam#data
|
|
http://www.w3.org/2000/01/rdf-schema#label
|
Protein interaction data
|
|
http://edamontology.org/created_in
|
beta12orEarlier
|
|
http://www.geneontology.org/formats/oboInOwl#hasNarrowSynonym
|
Residue interaction data |
| Atom interaction data |
| Protein non-covalent interactions report
|
|
http://www.geneontology.org/formats/oboInOwl#hasDefinition
|
Data concerning the interactions (predicted or known) within or between a protein, structural domain or part of a protein. This includes intra- and inter-residue contacts and distances, as well as interactions with other proteins and non-protein entities such as nucleic acid, metal atoms, water, ions etc.
|
|
http://www.w3.org/1999/02/22-rdf-syntax-ns#type
|
http://www.w3.org/2002/07/owl#Class
|
|
http://www.geneontology.org/formats/oboInOwl#hasExactSynonym
|
Protein interaction record |
| Protein report (interaction) |
| Protein-protein interaction data |
| Protein interaction report
|
|
http://www.w3.org/2000/01/rdf-schema#subClassOf
|
_:267 |
| http://edamontology.org/data_0897
|
http://edamontology.org/data_0006 |
|
http://www.geneontology.org/formats/oboInOwl#inSubset
|
http://purl.obolibrary.org/obo/edam#edam |
| http://purl.obolibrary.org/obo/edam#data
|
|
http://edamontology.org/notRecommendedForAnnotation
|
true
|
|
http://www.w3.org/2000/01/rdf-schema#label
|
Data
|
|
http://edamontology.org/created_in
|
beta12orEarlier
|
|
http://www.geneontology.org/formats/oboInOwl#hasNarrowSynonym
|
Datum |
| Data set
|
|
http://www.w3.org/2000/01/rdf-schema#seeAlso
|
http://www.ifomis.org/bfo/1.1/snap#Continuant |
| http://purl.org/biotop/biotop.owl#DigitalEntity |
| http://wsio.org/data_002 |
| "http://purl.obolibrary.org/obo/IAO_0000027" |
| http://semanticscience.org/resource/SIO_000069 |
| http://semanticscience.org/resource/SIO_000088 |
| "http://purl.obolibrary.org/obo/IAO_0000030" |
| http://www.onto-med.de/ontologies/gfo.owl#Perpetuant
|
|
http://www.geneontology.org/formats/oboInOwl#hasDefinition
|
Information, represented in an information artefact (data record) that is 'understandable' by dedicated computational tools that can use the data as input or produce it as output.
|
|
http://www.w3.org/1999/02/22-rdf-syntax-ns#type
|
http://www.w3.org/2002/07/owl#Class
|
|
http://www.w3.org/2002/07/owl#disjointWith
|
http://www.w3.org/2002/07/owl#DeprecatedClass |
| http://edamontology.org/operation_0004 |
| http://edamontology.org/format_1915 |
| http://edamontology.org/topic_0003
|
|
http://www.geneontology.org/formats/oboInOwl#hasExactSynonym
|
Data record
|
http://edamontology.org/operation_3092 |
|
http://www.geneontology.org/formats/oboInOwl#inSubset
|
http://purl.obolibrary.org/obo/edam#edam |
| http://purl.obolibrary.org/obo/edam#operations
|
|
http://www.w3.org/2000/01/rdf-schema#label
|
Protein feature detection
|
|
http://edamontology.org/created_in
|
beta13
|
|
http://www.geneontology.org/formats/oboInOwl#hasNarrowSynonym
|
Protein site recognition |
| Sequence feature detection (protein) |
| Sequence profile database search |
| Protein site detection |
| Protein site prediction |
| Protein secondary database search
|
|
http://www.geneontology.org/formats/oboInOwl#hasDefinition
|
Predict, recognise and identify positional features in proteins from analysing protein sequences or structures.
|
|
http://www.w3.org/1999/02/22-rdf-syntax-ns#type
|
http://www.w3.org/2002/07/owl#Class
|
|
http://www.geneontology.org/formats/oboInOwl#hasExactSynonym
|
Protein feature prediction |
| Protein feature recognition
|
|
http://www.w3.org/2000/01/rdf-schema#comment
|
Features includes functional sites or regions, secondary structure, structural domains and so on. Methods might use fingerprints, motifs, profiles, hidden Markov models, sequence alignment etc to provide a mapping of a query protein sequence to a discriminatory element. This includes methods that search a secondary protein database (Prosite, Blocks, ProDom, Prints, Pfam etc.) to assign a protein sequence(s) to a known protein family or group.
|
|
http://www.w3.org/2000/01/rdf-schema#subClassOf
|
_:274 |
| _:275 |
| http://edamontology.org/operation_2479 |
| http://edamontology.org/operation_2423 |
| _:276
|
http://edamontology.org/format_3884 |
|
http://www.w3.org/2000/01/rdf-schema#label
|
FF parameter format
|
|
http://edamontology.org/created_in
|
1.22
|
|
http://www.geneontology.org/formats/oboInOwl#hasDefinition
|
Format of force field parameter files, which store the set of parameters (charges, masses, radii, bond lengths, bond dihedrals, etc.) that are essential for the proper description and simulation of a molecular system.
|
|
http://www.w3.org/1999/02/22-rdf-syntax-ns#type
|
http://www.w3.org/2002/07/owl#Class
|
|
http://www.w3.org/2000/01/rdf-schema#comment
|
Many different file formats exist describing force field parameters. Tipically, each MD package or simulation software works with their own implementation (e.g. GROMACS itp, CHARMM rtf, AMBER off / frcmod).
|
|
http://www.w3.org/2000/01/rdf-schema#subClassOf
|
http://edamontology.org/format_2350 |
| _:285
|
http://edamontology.org/data_3108 |
|
http://www.geneontology.org/formats/oboInOwl#inSubset
|
http://purl.obolibrary.org/obo/edam#edam |
| http://purl.obolibrary.org/obo/edam#data
|
|
http://www.w3.org/2000/01/rdf-schema#label
|
Experimental measurement
|
|
http://edamontology.org/created_in
|
beta13
|
|
http://www.geneontology.org/formats/oboInOwl#hasNarrowSynonym
|
Measurement metadata |
| Raw experimental data
|
|
http://www.geneontology.org/formats/oboInOwl#hasDefinition
|
Raw data such as measurements or other results from laboratory experiments, as generated from laboratory hardware.
|
|
http://www.w3.org/1999/02/22-rdf-syntax-ns#type
|
http://www.w3.org/2002/07/owl#Class
|
|
http://www.geneontology.org/formats/oboInOwl#hasExactSynonym
|
Experimental measurement data |
| Measurement |
| Experimentally measured data |
| Measurement data |
| Measured data
|
|
http://www.w3.org/2000/01/rdf-schema#comment
|
This is a broad data type and is used a placeholder for other, more specific types. It is primarily intended to help navigation of EDAM and would not typically be used for annotation.
|
|
http://www.w3.org/2000/01/rdf-schema#subClassOf
|
http://edamontology.org/data_0006
|
http://edamontology.org/format_3879 |
|
http://www.geneontology.org/formats/oboInOwl#inSubset
|
http://purl.obolibrary.org/obo/edam#formats |
| http://purl.obolibrary.org/obo/edam#edam
|
|
http://edamontology.org/notRecommendedForAnnotation
|
true
|
|
http://www.w3.org/2000/01/rdf-schema#label
|
Topology format
|
|
http://edamontology.org/created_in
|
1.22
|
|
http://www.geneontology.org/formats/oboInOwl#hasNarrowSynonym
|
MD topology format |
| Protein topology format |
| NA topology format |
| CG topology format
|
|
http://www.geneontology.org/formats/oboInOwl#hasDefinition
|
Format of topology files; containing the static information of a structure molecular system that is needed for a molecular simulation.
|
|
http://www.w3.org/1999/02/22-rdf-syntax-ns#type
|
http://www.w3.org/2002/07/owl#Class
|
|
http://www.w3.org/2000/01/rdf-schema#comment
|
Many different file formats exist describing structural molecular topology. Tipically, each MD package or simulation software works with their own implementation (e.g. GROMACS top, CHARMM psf, AMBER prmtop).
|
|
http://www.w3.org/2000/01/rdf-schema#subClassOf
|
_:294 |
| http://edamontology.org/format_2350
|
http://edamontology.org/data_0897 |
|
http://www.geneontology.org/formats/oboInOwl#inSubset
|
http://purl.obolibrary.org/obo/edam#edam |
| http://purl.obolibrary.org/obo/edam#data
|
|
http://www.w3.org/2000/01/rdf-schema#label
|
Protein property
|
|
http://edamontology.org/created_in
|
beta12orEarlier
|
|
http://www.geneontology.org/formats/oboInOwl#hasNarrowSynonym
|
Protein sequence statistics
|
|
http://www.geneontology.org/formats/oboInOwl#hasDefinition
|
A report of primarily non-positional data describing intrinsic physical, chemical or other properties of a protein molecule or model.
|
|
http://www.w3.org/1999/02/22-rdf-syntax-ns#type
|
http://www.w3.org/2002/07/owl#Class
|
|
http://www.geneontology.org/formats/oboInOwl#hasExactSynonym
|
Protein properties |
| Protein physicochemical property
|
|
http://www.w3.org/2000/01/rdf-schema#comment
|
This is a broad data type and is used a placeholder for other, more specific types. Data may be based on analysis of nucleic acid sequence or structural data, for example reports on the surface properties (shape, hydropathy, electrostatic patches etc) of a protein structure, protein flexibility or motion, and protein architecture (spatial arrangement of secondary structure).
|
|
http://www.w3.org/2000/01/rdf-schema#subClassOf
|
http://edamontology.org/data_2087
|
http://edamontology.org/data_2603 |
|
http://www.geneontology.org/formats/oboInOwl#inSubset
|
http://purl.obolibrary.org/obo/edam#edam |
| http://purl.obolibrary.org/obo/edam#data
|
|
http://www.w3.org/2000/01/rdf-schema#label
|
Expression data
|
|
http://edamontology.org/created_in
|
beta12orEarlier
|
|
http://www.geneontology.org/formats/oboInOwl#hasNarrowSynonym
|
Microarray data |
| Gene transcription profile |
| Non-coding RNA profile |
| RNA-seq data |
| Gene product quantification data |
| Non-coding RNA quantification data |
| Metabolite expression data |
| mRNA quantification data |
| RNA profile |
| Transcriptome profile |
| RNA quantification data |
| mRNA profile |
| Transcriptome quantification data |
| Gene product profile |
| Gene transcription quantification data |
| Protein expression data |
| Gene expression data
|
|
http://www.geneontology.org/formats/oboInOwl#hasDefinition
|
Image, hybridisation or some other data arising from a study of feature/molecule expression, typically profiling or quantification.
|
|
http://www.w3.org/1999/02/22-rdf-syntax-ns#type
|
http://www.w3.org/2002/07/owl#Class
|
|
http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym
|
Protein quantification data |
| Protein profile |
| Proteome profile |
| Proteome quantification data
|
|
http://www.w3.org/2000/01/rdf-schema#subClassOf
|
_:305 |
| http://edamontology.org/data_0006
|
http://edamontology.org/topic_0736 |
|
http://www.geneontology.org/formats/oboInOwl#inSubset
|
http://purl.obolibrary.org/obo/edam#topics |
| http://purl.obolibrary.org/obo/edam#edam
|
|
http://edamontology.org/isdebtag
|
true
|
|
http://www.w3.org/2000/01/rdf-schema#label
|
Protein folds and structural domains
|
|
http://edamontology.org/created_in
|
beta12orEarlier
|
|
http://www.geneontology.org/formats/oboInOwl#hasNarrowSynonym
|
Protein transmembrane regions |
| Protein folds |
| Transmembrane regions |
| Protein membrane regions |
| Protein topological domains |
| Protein structural domains |
| Intramembrane regions |
| Protein domains
|
|
http://www.geneontology.org/formats/oboInOwl#hasDefinition
|
Protein tertiary structural domains and folds in a protein or polypeptide chain.
|
|
http://www.w3.org/1999/02/22-rdf-syntax-ns#type
|
http://www.w3.org/2002/07/owl#Class
|
|
http://www.w3.org/2000/01/rdf-schema#comment
|
This includes topological domains such as cytoplasmic regions in a protein. |
| This includes trans- or intra-membrane regions of a protein, typically describing physicochemical properties of the secondary structure elements. For example, the location and size of the membrane spanning segments and intervening loop regions, transmembrane region IN/OUT orientation relative to the membrane, plus the following data for each amino acid: A Z-coordinate (the distance to the membrane center), the free energy of membrane insertion (calculated in a sliding window over the sequence) and a reliability score. The z-coordinate implies information about re-entrant helices, interfacial helices, the tilt of a transmembrane helix and loop lengths.
|
|
http://www.w3.org/2000/01/rdf-schema#subClassOf
|
http://edamontology.org/topic_2814
|
|
http://www.geneontology.org/formats/oboInOwl#hasHumanReadableId
|
Protein_folds_and_structural_domains
|
http://edamontology.org/topic_0749 |
|
http://www.geneontology.org/formats/oboInOwl#inSubset
|
http://purl.obolibrary.org/obo/edam#topics |
| http://purl.obolibrary.org/obo/edam#edam
|
|
http://www.w3.org/2000/01/rdf-schema#label
|
Transcription factors and regulatory sites
|
|
http://edamontology.org/created_in
|
beta12orEarlier
|
|
http://www.geneontology.org/formats/oboInOwl#hasNarrowSynonym
|
Enhancers |
| Promoters |
| CpG islands |
| TATA signals |
| Transcriptional regulatory sites |
| Transcription factor binding sites |
| CCAAT box |
| Attenuators |
| CAAT signals |
| Transcription factors |
| GC signals |
| Isochores |
| Terminators |
| CAT box |
| TFBS |
| -10 signals |
| -35 signals
|
|
http://www.w3.org/2000/01/rdf-schema#seeAlso
|
https://en.wikipedia.org/wiki/Transcription_factor |
| https://en.wikipedia.org/wiki/Transcriptional_regulation
|
|
http://www.geneontology.org/formats/oboInOwl#hasDefinition
|
Proteins that bind to DNA and control transcription of DNA to mRNA (transcription factors) and also transcriptional regulatory sites, elements and regions (such as promoters, enhancers, silencers and boundary elements / insulators) in nucleotide sequences.
|
|
http://www.w3.org/1999/02/22-rdf-syntax-ns#type
|
http://www.w3.org/2002/07/owl#Class
|
|
http://www.w3.org/2000/01/rdf-schema#comment
|
This includes promoters, CAAT signals, TATA signals, -35 signals, -10 signals, GC signals, primer binding sites for initiation of transcription or reverse transcription, enhancer, attenuator, terminators and ribosome binding sites. |
| Transcription factor proteins either promote (as an activator) or block (as a repressor) the binding to DNA of RNA polymerase. Regulatory sites including transcription factor binding site as well as promoters, enhancers, silencers and boundary elements / insulators. |
| This includes CpG rich regions (isochores) in a nucleotide sequence.
|
|
http://www.w3.org/2000/01/rdf-schema#subClassOf
|
http://edamontology.org/topic_0078 |
| http://edamontology.org/topic_0203 |
| http://edamontology.org/topic_3125
|
|
http://www.geneontology.org/formats/oboInOwl#hasHumanReadableId
|
Transcription_factors_and_regulatory_sites
|
http://edamontology.org/data_0857 |
|
http://www.geneontology.org/formats/oboInOwl#inSubset
|
http://purl.obolibrary.org/obo/edam#edam |
| http://purl.obolibrary.org/obo/edam#data
|
|
http://www.w3.org/2000/01/rdf-schema#label
|
Sequence search results
|
|
http://edamontology.org/created_in
|
beta12orEarlier
|
|
http://www.geneontology.org/formats/oboInOwl#hasDefinition
|
A report of sequence hits and associated data from searching a database of sequences (for example a BLAST search). This will typically include a list of scores (often with statistical evaluation) and a set of alignments for the hits.
|
|
http://www.w3.org/1999/02/22-rdf-syntax-ns#type
|
http://www.w3.org/2002/07/owl#Class
|
|
http://www.geneontology.org/formats/oboInOwl#hasExactSynonym
|
Sequence database hits |
| Sequence search hits |
| Sequence database search results |
| |
| Database hits (sequence)
|
|
http://www.w3.org/2000/01/rdf-schema#comment
|
The score list includes the alignment score, percentage of the query sequence matched, length of the database sequence entry in this alignment, identifier of the database sequence entry, excerpt of the database sequence entry description etc.
|
|
http://www.w3.org/2000/01/rdf-schema#subClassOf
|
http://edamontology.org/data_2080
|
http://edamontology.org/data_0850 |
|
http://www.geneontology.org/formats/oboInOwl#inSubset
|
http://purl.obolibrary.org/obo/edam#edam |
| http://purl.obolibrary.org/obo/edam#data
|
|
http://www.w3.org/2000/01/rdf-schema#label
|
Sequence set
|
|
http://edamontology.org/created_in
|
beta12orEarlier
|
|
http://www.geneontology.org/formats/oboInOwl#hasNarrowSynonym
|
Alignment reference
|
|
http://www.geneontology.org/formats/oboInOwl#hasDefinition
|
A collection of one or typically multiple molecular sequences (which can include derived data or metadata) that do not (typically) correspond to molecular sequence database records or entries and which (typically) are derived from some analytical method.
|
|
http://www.w3.org/1999/02/22-rdf-syntax-ns#type
|
http://www.w3.org/2002/07/owl#Class
|
|
http://www.w3.org/2000/01/rdf-schema#comment
|
An example is an alignment reference; one or a set of reference molecular sequences, structures, or profiles used for alignment of genomic, transcriptomic, or proteomic experimental data. |
| This concept may be used for arbitrary sequence sets and associated data arising from processing.
|
|
http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym
|
SO:0001260
|
|
http://www.w3.org/2000/01/rdf-schema#subClassOf
|
http://edamontology.org/data_0006
|
http://edamontology.org/data_0858 |
|
http://www.geneontology.org/formats/oboInOwl#inSubset
|
http://purl.obolibrary.org/obo/edam#edam |
| http://purl.obolibrary.org/obo/edam#data
|
|
http://www.w3.org/2000/01/rdf-schema#label
|
Sequence signature matches
|
|
http://edamontology.org/created_in
|
beta12orEarlier
|
|
http://www.geneontology.org/formats/oboInOwl#hasNarrowSynonym
|
Protein secondary database search results |
| Search results (protein secondary database)
|
|
http://www.geneontology.org/formats/oboInOwl#hasDefinition
|
Report on the location of matches in one or more sequences to profiles, motifs (conserved or functional patterns) or other signatures.
|
|
http://www.w3.org/1999/02/22-rdf-syntax-ns#type
|
http://www.w3.org/2002/07/owl#Class
|
|
http://www.geneontology.org/formats/oboInOwl#hasExactSynonym
|
Sequence profile matches |
| Sequence motif matches
|
|
http://www.w3.org/2000/01/rdf-schema#comment
|
This ncluding reports of hits from a search of a protein secondary or domain database.
|
|
http://www.w3.org/2000/01/rdf-schema#subClassOf
|
http://edamontology.org/data_0860
|
http://edamontology.org/data_0848 |
|
http://www.geneontology.org/formats/oboInOwl#inSubset
|
http://purl.obolibrary.org/obo/edam#obsolete
|
|
http://www.w3.org/2002/07/owl#deprecated
|
true
|
|
http://www.w3.org/2000/01/rdf-schema#label
|
Raw sequence
|
|
http://edamontology.org/created_in
|
beta12orEarlier
|
|
http://edamontology.org/deprecation_comment
|
Deprecated because this is bloat / confusing & better handled as an EDAM Format concept - "raw" sequences just imply a particular format (i.e. one with a vanilla string, possible in a particular alphabet, with no metadata).
|
|
http://www.geneontology.org/formats/oboInOwl#hasDefinition
|
A raw molecular sequence (string of characters) which might include ambiguity, unknown positions and non-sequence characters.
|
|
http://www.w3.org/1999/02/22-rdf-syntax-ns#type
|
http://www.w3.org/2002/07/owl#Class
|
|
http://www.geneontology.org/formats/oboInOwl#replacedBy
|
http://edamontology.org/data_2044
|
|
http://www.w3.org/2000/01/rdf-schema#comment
|
Non-sequence characters may be used for example for gaps and translation stop.
|
|
http://www.w3.org/2000/01/rdf-schema#subClassOf
|
http://www.w3.org/2002/07/owl#DeprecatedClass
|
|
http://edamontology.org/oldParent
|
http://edamontology.org/data_2044
|
|
http://edamontology.org/obsolete_since
|
1.23
|
http://edamontology.org/data_0872 |
|
http://www.geneontology.org/formats/oboInOwl#inSubset
|
http://purl.obolibrary.org/obo/edam#edam |
| http://purl.obolibrary.org/obo/edam#data
|
|
http://www.geneontology.org/formats/oboInOwl#hasDbXref
|
Moby:Tree |
| Moby:phylogenetic_tree |
| Moby:myTree
|
|
http://www.w3.org/2000/01/rdf-schema#label
|
Phylogenetic tree
|
|
http://edamontology.org/created_in
|
beta12orEarlier
|
|
http://www.w3.org/2000/01/rdf-schema#seeAlso
|
http://www.evolutionaryontology.org/cdao.owl#Tree |
| http://purl.bioontology.org/ontology/MSH/D010802
|
|
http://www.geneontology.org/formats/oboInOwl#hasDefinition
|
The raw data (not just an image) from which a phylogenetic tree is directly generated or plotted, such as topology, lengths (in time or in expected amounts of variance) and a confidence interval for each length.
|
|
http://www.w3.org/1999/02/22-rdf-syntax-ns#type
|
http://www.w3.org/2002/07/owl#Class
|
|
http://www.geneontology.org/formats/oboInOwl#hasExactSynonym
|
Phylogeny
|
|
http://www.w3.org/2000/01/rdf-schema#comment
|
A phylogenetic tree is usually constructed from a set of sequences from which an alignment (or data matrix) is calculated. See also 'Phylogenetic tree image'.
|
|
http://www.w3.org/2000/01/rdf-schema#subClassOf
|
http://edamontology.org/data_2523 |
| _:329
|
http://edamontology.org/data_0871 |
|
http://www.geneontology.org/formats/oboInOwl#inSubset
|
http://purl.obolibrary.org/obo/edam#edam |
| http://purl.obolibrary.org/obo/edam#data
|
|
http://www.w3.org/2000/01/rdf-schema#label
|
Phylogenetic character data
|
|
http://edamontology.org/created_in
|
beta12orEarlier
|
|
http://www.w3.org/2000/01/rdf-schema#seeAlso
|
http://www.evolutionaryontology.org/cdao.owl#Character
|
|
http://www.geneontology.org/formats/oboInOwl#hasDefinition
|
Basic character data from which a phylogenetic tree may be generated.
|
|
http://www.w3.org/1999/02/22-rdf-syntax-ns#type
|
http://www.w3.org/2002/07/owl#Class
|
|
http://www.w3.org/2000/01/rdf-schema#comment
|
As defined, this concept would also include molecular sequences, microsatellites, polymorphisms (RAPDs, RFLPs, or AFLPs), restriction sites and fragments
|
|
http://www.w3.org/2000/01/rdf-schema#subClassOf
|
http://edamontology.org/data_2523
|
http://edamontology.org/operation_3196 |
|
http://www.geneontology.org/formats/oboInOwl#inSubset
|
http://purl.obolibrary.org/obo/edam#edam |
| http://purl.obolibrary.org/obo/edam#operations
|
|
http://www.w3.org/2000/01/rdf-schema#label
|
Genotyping
|
|
http://edamontology.org/created_in
|
1.1
|
|
http://www.geneontology.org/formats/oboInOwl#hasDefinition
|
Analyse DNA sequence data to identify differences between the genetic composition (genotype) of an individual compared to other individual's or a reference sequence.
|
|
http://www.w3.org/1999/02/22-rdf-syntax-ns#type
|
http://www.w3.org/2002/07/owl#Class
|
|
http://www.w3.org/2000/01/rdf-schema#comment
|
Methods might consider cytogenetic analyses, copy number polymorphism (and calculate copy number calls for copy-number variation(CNV) regions), single nucleotide polymorphism (SNP), , rare copy number variation (CNV) identification, loss of heterozygosity data and so on.
|
|
http://www.w3.org/2000/01/rdf-schema#subClassOf
|
http://edamontology.org/operation_3197
|
http://edamontology.org/operation_3197 |
|
http://www.geneontology.org/formats/oboInOwl#inSubset
|
http://purl.obolibrary.org/obo/edam#edam |
| http://purl.obolibrary.org/obo/edam#operations
|
|
http://www.w3.org/2000/01/rdf-schema#label
|
Genetic variation analysis
|
|
http://edamontology.org/created_in
|
1.1
|
|
http://www.geneontology.org/formats/oboInOwl#hasDefinition
|
Analyse a genetic variation, for example to annotate its location, alleles, classification, and effects on individual transcripts predicted for a gene model.
|
|
http://www.w3.org/1999/02/22-rdf-syntax-ns#type
|
http://www.w3.org/2002/07/owl#Class
|
|
http://www.geneontology.org/formats/oboInOwl#hasExactSynonym
|
Genetic variation annotation |
| Variant analysis |
| Sequence variation analysis
|
|
http://www.w3.org/2000/01/rdf-schema#comment
|
Genetic variation annotation provides contextual interpretation of coding SNP consequences in transcripts. It allows comparisons to be made between variation data in different populations or strains for the same transcript.
|
|
http://www.w3.org/2000/01/rdf-schema#subClassOf
|
http://edamontology.org/operation_2945
|
http://edamontology.org/operation_3198 |
|
http://www.geneontology.org/formats/oboInOwl#inSubset
|
http://purl.obolibrary.org/obo/edam#edam |
| http://purl.obolibrary.org/obo/edam#operations
|
|
http://www.w3.org/2000/01/rdf-schema#label
|
Read mapping
|
|
http://edamontology.org/created_in
|
1.1
|
|
http://www.geneontology.org/formats/oboInOwl#hasDefinition
|
Align short oligonucleotide sequences (reads) to a larger (genomic) sequence.
|
|
http://www.w3.org/1999/02/22-rdf-syntax-ns#type
|
http://www.w3.org/2002/07/owl#Class
|
|
http://www.geneontology.org/formats/oboInOwl#hasExactSynonym
|
Oligonucleotide alignment construction |
| Oligonucleotide mapping |
| Oligonucleotide alignment generation |
| Short oligonucleotide alignment |
| Short sequence read mapping |
| Read alignment |
| Short read alignment |
| Oligonucleotide alignment |
| Short read mapping
|
|
http://www.w3.org/2000/01/rdf-schema#comment
|
The purpose of read mapping is to identify the location of sequenced fragments within a reference genome and assumes that there is, in fact, at least local similarity between the fragment and reference sequences.
|
|
http://www.w3.org/2000/01/rdf-schema#subClassOf
|
http://edamontology.org/operation_2944 |
| http://edamontology.org/operation_0292
|
http://edamontology.org/operation_3192 |
|
http://www.geneontology.org/formats/oboInOwl#inSubset
|
http://purl.obolibrary.org/obo/edam#edam |
| http://purl.obolibrary.org/obo/edam#operations
|
|
http://www.w3.org/2000/01/rdf-schema#label
|
Sequence trimming
|
|
http://edamontology.org/created_in
|
1.1
|
|
http://www.geneontology.org/formats/oboInOwl#hasNarrowSynonym
|
Trim to reference |
| Barcode sequence removal |
| Trim ends |
| Trim vector
|
|
http://www.geneontology.org/formats/oboInOwl#hasDefinition
|
Cut (remove) the end from a molecular sequence.
|
|
http://www.w3.org/1999/02/22-rdf-syntax-ns#type
|
http://www.w3.org/2002/07/owl#Class
|
|
http://www.geneontology.org/formats/oboInOwl#hasExactSynonym
|
Trimming
|
|
http://www.w3.org/2000/01/rdf-schema#comment
|
This includes
ennd trimming
Trim sequences (typically from an automated DNA sequencer) to remove misleading ends.
For example trim polyA tails, introns and primer sequence flanking the sequence of amplified exons, or other unwanted sequence.
trimming to a reference sequence,
Trim sequences (typically from an automated DNA sequencer) to remove the sequence ends that extend beyond an assembled reference sequence.
vector trimming
Trim sequences (typically from an automated DNA sequencer) to remove sequence-specific end regions, typically contamination from vector sequences.
|
|
http://www.w3.org/2000/01/rdf-schema#subClassOf
|
http://edamontology.org/operation_0369
|
http://edamontology.org/is_output_of |
|
http://purl.obolibrary.org/obo/is_anti_symmetric
|
false
|
|
http://www.w3.org/2000/01/rdf-schema#label
|
is output of
|
|
http://purl.obolibrary.org/obo/is_reflexive
|
false
|
|
http://www.geneontology.org/formats/oboInOwl#isCyclic
|
true
|
|
http://www.w3.org/2000/01/rdf-schema#range
|
http://edamontology.org/operation_0004
|
|
http://www.geneontology.org/formats/oboInOwl#inSubset
|
edam |
| relations
|
|
http://purl.obolibrary.org/obo/is_symmetric
|
false
|
|
http://www.w3.org/2000/01/rdf-schema#domain
|
http://edamontology.org/data_0006
|
|
http://www.w3.org/2000/01/rdf-schema#seeAlso
|
http://wsio.org/is_output_of |
| "http://purl.obolibrary.org/obo/OBI_0000312"
|
|
http://www.geneontology.org/formats/oboInOwl#hasDefinition
|
'A is_output_of B' defines for the subject A, that it as a necessary or actual output or output argument of the object B.
|
|
http://www.w3.org/1999/02/22-rdf-syntax-ns#type
|
http://www.w3.org/2002/07/owl#ObjectProperty
|
|
http://www.w3.org/2000/01/rdf-schema#comment
|
Subject A can be any concept or entity outside of an ontology (or an ontology concept in a role of an entity being semantically annotated). Object B can either be a concept that is or has an 'Operation' function, or an entity outside of an ontology that has an 'Operation' function or is an 'Operation'. In EDAM, 'is_output_of' is not explicitly defined between EDAM concepts, only the inverse 'has_output'.
|
|
http://purl.obolibrary.org/obo/transitive_over
|
OBO_REL:is_a
|
|
http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym
|
OBO_REL:participates_in
|
http://edamontology.org/data_1255 |
|
http://www.geneontology.org/formats/oboInOwl#inSubset
|
http://purl.obolibrary.org/obo/edam#edam |
| http://purl.obolibrary.org/obo/edam#data
|
|
http://www.w3.org/2000/01/rdf-schema#label
|
Sequence features
|
|
http://edamontology.org/created_in
|
beta12orEarlier
|
|
http://www.w3.org/2000/01/rdf-schema#seeAlso
|
http://purl.bioontology.org/ontology/MSH/D058977
|
|
http://www.geneontology.org/formats/oboInOwl#hasDefinition
|
Annotation of positional features of molecular sequence(s), i.e. that can be mapped to position(s) in the sequence.
|
|
http://www.w3.org/1999/02/22-rdf-syntax-ns#type
|
http://www.w3.org/2002/07/owl#Class
|
|
http://www.geneontology.org/formats/oboInOwl#hasExactSynonym
|
Sequence features report |
| Feature record |
| Features |
| General sequence features
|
|
http://www.w3.org/2000/01/rdf-schema#comment
|
This includes annotation of positional sequence features, organised into a standard feature table, or any other report of sequence features. General feature reports are a source of sequence feature table information although internal conversion would be required.
|
|
http://www.w3.org/2000/01/rdf-schema#subClassOf
|
http://edamontology.org/data_0006
|
|
http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym
|
SO:0000110
|
http://edamontology.org/data_1278 |
|
http://www.geneontology.org/formats/oboInOwl#inSubset
|
http://purl.obolibrary.org/obo/edam#edam |
| http://purl.obolibrary.org/obo/edam#data
|
|
http://www.geneontology.org/formats/oboInOwl#hasDbXref
|
Moby:GeneticMap
|
|
http://www.w3.org/2000/01/rdf-schema#label
|
Genetic map
|
|
http://edamontology.org/created_in
|
beta12orEarlier
|
|
http://www.geneontology.org/formats/oboInOwl#hasDefinition
|
A map showing the relative positions of genetic markers in a nucleic acid sequence, based on estimation of non-physical distance such as recombination frequencies.
|
|
http://www.w3.org/1999/02/22-rdf-syntax-ns#type
|
http://www.w3.org/2002/07/owl#Class
|
|
http://www.geneontology.org/formats/oboInOwl#hasExactSynonym
|
Linkage map
|
|
http://www.w3.org/2000/01/rdf-schema#comment
|
A genetic (linkage) map indicates the proximity of two genes on a chromosome, whether two genes are linked and the frequency they are transmitted together to an offspring. They are limited to genetic markers of traits observable only in whole organisms.
|
|
http://www.w3.org/2000/01/rdf-schema#subClassOf
|
http://edamontology.org/data_1274
|
http://edamontology.org/topic_3068 |
|
http://www.geneontology.org/formats/oboInOwl#inSubset
|
http://purl.obolibrary.org/obo/edam#events |
| http://purl.obolibrary.org/obo/edam#topics |
| http://purl.obolibrary.org/obo/edam#edam
|
|
http://edamontology.org/isdebtag
|
true
|
|
http://www.w3.org/2000/01/rdf-schema#label
|
Literature and language
|
|
http://edamontology.org/created_in
|
beta13
|
|
http://www.geneontology.org/formats/oboInOwl#hasNarrowSynonym
|
Scientific literature |
| Bibliography |
| References |
| Citations |
| Documentation
|
|
http://www.w3.org/2000/01/rdf-schema#seeAlso
|
http://purl.bioontology.org/ontology/MSH/D011642
|
|
http://www.geneontology.org/formats/oboInOwl#hasDefinition
|
The scientific literature, language processing, reference information, and documentation.
|
|
http://www.w3.org/1999/02/22-rdf-syntax-ns#type
|
http://www.w3.org/2002/07/owl#Class
|
|
http://www.geneontology.org/formats/oboInOwl#hasExactSynonym
|
Language |
| Literature
|
|
http://www.w3.org/2000/01/rdf-schema#comment
|
This includes the documentation of resources such as tools, services and databases, user support, how to get help etc.
|
|
http://www.geneontology.org/formats/oboInOwl#hasHumanReadableId
|
Literature_and_language
|
|
http://www.w3.org/2000/01/rdf-schema#subClassOf
|
http://edamontology.org/topic_0003
|
http://edamontology.org/topic_3070 |
|
http://www.geneontology.org/formats/oboInOwl#hasDbXref
|
VT 1.5.99 Other |
| VT 1.5.3 Behavioural biology |
| VT 1.5.1 Aerobiology |
| VT 1.5.7 Biological rhythm |
| VT 1.5 Biological sciences |
| VT 1.5.13 Cryobiology |
| VT 1.5.8 Biology |
| VT 1.5.23 Reproductive biology
|
|
http://edamontology.org/isdebtag
|
true
|
|
http://www.w3.org/2000/01/rdf-schema#label
|
Biology
|
|
http://edamontology.org/created_in
|
beta13
|
|
http://www.geneontology.org/formats/oboInOwl#hasExactSynonym
|
Biological science
|
|
http://www.geneontology.org/formats/oboInOwl#inSubset
|
http://purl.obolibrary.org/obo/edam#events |
| http://purl.obolibrary.org/obo/edam#topics |
| http://purl.obolibrary.org/obo/edam#edam
|
|
http://www.geneontology.org/formats/oboInOwl#hasNarrowSynonym
|
Cryobiology |
| Biological rhythms |
| Behavioural biology |
| Chronobiology |
| Reproductive biology |
| Aerobiology
|
|
http://www.w3.org/2000/01/rdf-schema#seeAlso
|
https://en.wikipedia.org/wiki/Biology
|
|
http://www.geneontology.org/formats/oboInOwl#hasDefinition
|
The study of life and living organisms, including their morphology, biochemistry, physiology, development, evolution, and so on.
|
|
http://www.w3.org/1999/02/22-rdf-syntax-ns#type
|
http://www.w3.org/2002/07/owl#Class
|
|
http://www.geneontology.org/formats/oboInOwl#hasHumanReadableId
|
Biology
|
|
http://www.w3.org/2000/01/rdf-schema#subClassOf
|
http://edamontology.org/topic_0003
|
|
http://www.geneontology.org/formats/oboInOwl#hasBroadSynonym
|
Life sciences |
| Life science
|
http://edamontology.org/data_2535 |
|
http://www.geneontology.org/formats/oboInOwl#inSubset
|
http://purl.obolibrary.org/obo/edam#edam |
| http://purl.obolibrary.org/obo/edam#data
|
|
http://www.w3.org/2000/01/rdf-schema#label
|
Sequence tag profile
|
|
http://edamontology.org/created_in
|
beta12orEarlier
|
|
http://www.geneontology.org/formats/oboInOwl#hasNarrowSynonym
|
Sequence tag profile (with gene assignment)
|
|
http://www.geneontology.org/formats/oboInOwl#hasDefinition
|
Output from a serial analysis of gene expression (SAGE), massively parallel signature sequencing (MPSS) or sequencing by synthesis (SBS) experiment. In all cases this is a list of short sequence tags and the number of times it is observed.
|
|
http://www.w3.org/1999/02/22-rdf-syntax-ns#type
|
http://www.w3.org/2002/07/owl#Class
|
|
http://www.geneontology.org/formats/oboInOwl#hasExactSynonym
|
Sequencing-based expression profile
|
|
http://www.w3.org/2000/01/rdf-schema#comment
|
This includes tag to gene assignments (tag mapping) of SAGE, MPSS and SBS data. Typically this is the sequencing-based expression profile annotated with gene identifiers. |
| SAGE, MPSS and SBS experiments are usually performed to study gene expression. The sequence tags are typically subsequently annotated (after a database search) with the mRNA (and therefore gene) the tag was extracted from.
|
|
http://www.w3.org/2000/01/rdf-schema#subClassOf
|
http://edamontology.org/data_0928
|
http://edamontology.org/data_2526 |
|
http://www.geneontology.org/formats/oboInOwl#inSubset
|
http://purl.obolibrary.org/obo/edam#edam |
| http://purl.obolibrary.org/obo/edam#data
|
|
http://www.w3.org/2000/01/rdf-schema#label
|
Text data
|
|
http://edamontology.org/created_in
|
beta12orEarlier
|
|
http://www.geneontology.org/formats/oboInOwl#hasNarrowSynonym
|
Scientific text data |
| Article data
|
|
http://www.geneontology.org/formats/oboInOwl#hasDefinition
|
Data concerning, extracted from, or derived from the analysis of a scientific text (or texts) such as a full text article from a scientific journal.
|
|
http://www.w3.org/1999/02/22-rdf-syntax-ns#type
|
http://www.w3.org/2002/07/owl#Class
|
|
http://www.w3.org/2000/01/rdf-schema#comment
|
This is a broad data type and is used a placeholder for other, more specific types. It is primarily intended to help navigation of EDAM and would not typically be used for annotation. It includes concepts that are best described as scientific text or closely concerned with or derived from text.
|
|
http://www.w3.org/2000/01/rdf-schema#subClassOf
|
_:364 |
| http://edamontology.org/data_0006
|
http://edamontology.org/operation_0004 |
|
http://www.geneontology.org/formats/oboInOwl#inSubset
|
http://purl.obolibrary.org/obo/edam#edam |
| http://purl.obolibrary.org/obo/edam#operations
|
|
http://edamontology.org/notRecommendedForAnnotation
|
true
|
|
http://www.w3.org/2000/01/rdf-schema#label
|
Operation
|
|
http://edamontology.org/created_in
|
beta12orEarlier
|
|
http://www.geneontology.org/formats/oboInOwl#hasNarrowSynonym
|
Computational subroutine |
| Mathematical function |
| Function (programming) |
| Computational procedure |
| Lambda abstraction |
| Computational operation |
| Computational method |
| Mathematical operation
|
|
http://www.w3.org/2000/01/rdf-schema#seeAlso
|
http://en.wikipedia.org/wiki/Subroutine |
| http://wsio.org/operation_001 |
| http://semanticscience.org/resource/SIO_000649 |
| http://www.ifomis.org/bfo/1.1/snap#Quality |
| http://en.wikipedia.org/wiki/Function_(mathematics) |
| http://en.wikipedia.org/wiki/Function_(computer_science) |
| http://www.ifomis.org/bfo/1.1/snap#Continuant |
| http://semanticscience.org/resource/SIO_000017 |
| http://onto.eva.mpg.de/ontologies/gfo-bio.owl#Method |
| http://purl.org/biotop/biotop.owl#Function |
| http://www.ebi.ac.uk/swo/SWO_0000003 |
| http://www.loa-cnr.it/ontologies/DOLCE-Lite.owl#quality |
| http://www.onto-med.de/ontologies/gfo.owl#Process |
| http://www.ifomis.org/bfo/1.1/snap#Function |
| http://www.onto-med.de/ontologies/gfo.owl#Function |
| http://www.loa-cnr.it/ontologies/DOLCE-Lite.owl#process |
| http://www.ifomis.org/bfo/1.1/span#Process |
| http://www.onto-med.de/ontologies/gfo.owl#Perpetuant
|
|
http://www.geneontology.org/formats/oboInOwl#hasDefinition
|
A function that processes a set of inputs and results in a set of outputs, or associates arguments (inputs) with values (outputs).
|
|
http://www.w3.org/1999/02/22-rdf-syntax-ns#type
|
http://www.w3.org/2002/07/owl#Class
|
|
http://www.w3.org/2002/07/owl#disjointWith
|
http://www.w3.org/2002/07/owl#DeprecatedClass |
| http://edamontology.org/topic_0003
|
|
http://www.w3.org/2000/01/rdf-schema#comment
|
Special cases are: a) An operation that consumes no input (has no input arguments). Such operation is either a constant function, or an operation depending only on the underlying state. b) An operation that may modify the underlying state but has no output. c) The singular-case operation with no input or output, that still may modify the underlying state.
|
|
http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym
|
sumo:Function |
| Process |
| Computational tool
|
|
http://www.geneontology.org/formats/oboInOwl#hasBroadSynonym
|
Function
|
http://edamontology.org/topic_3511 |
|
http://www.geneontology.org/formats/oboInOwl#inSubset
|
http://purl.obolibrary.org/obo/edam#topics |
| http://purl.obolibrary.org/obo/edam#edam
|
|
http://www.w3.org/2000/01/rdf-schema#label
|
Nucleic acid sites, features and motifs
|
|
http://edamontology.org/created_in
|
1.8
|
|
http://www.geneontology.org/formats/oboInOwl#hasNarrowSynonym
|
Primer binding sites |
| Sequence tagged sites |
| Nucleic acid sequence features |
| Nucleic acid functional sites
|
|
http://www.geneontology.org/formats/oboInOwl#hasDefinition
|
The biology, archival, detection, prediction and analysis of positional features such as functional and other key sites, in nucleic acid sequences and the conserved patterns (motifs, profiles etc.) that may be used to describe them.
|
|
http://www.w3.org/1999/02/22-rdf-syntax-ns#type
|
http://www.w3.org/2002/07/owl#Class
|
|
http://www.w3.org/2000/01/rdf-schema#comment
|
Sequence tagged sites are short DNA sequences that are unique within a genome and serve as a mapping landmark, detectable by PCR they allow a genome to be mapped via an ordering of STSs.
|
|
http://www.geneontology.org/formats/oboInOwl#hasHumanReadableId
|
Nucleic_acid_sites_features_and_motifs
|
|
http://www.w3.org/2000/01/rdf-schema#subClassOf
|
http://edamontology.org/topic_0160 |
| http://edamontology.org/topic_0077
|
http://edamontology.org/topic_3512 |
|
http://www.geneontology.org/formats/oboInOwl#inSubset
|
http://purl.obolibrary.org/obo/edam#topics |
| http://purl.obolibrary.org/obo/edam#edam
|
|
http://www.w3.org/2000/01/rdf-schema#label
|
Gene transcripts
|
|
http://edamontology.org/created_in
|
1.8
|
|
http://www.geneontology.org/formats/oboInOwl#hasNarrowSynonym
|
Gene transcript features |
| Signal peptide coding sequence |
| Fusion transcripts |
| mRNA |
| PolyA signal |
| Transit peptide coding sequence |
| Coding RNA |
| EST |
| Introns |
| PolyA site |
| cDNA |
| Exons
|
|
http://www.geneontology.org/formats/oboInOwl#hasDefinition
|
Transcription of DNA into RNA and features of a messenger RNA (mRNA) molecules including precursor RNA, primary (unprocessed) transcript and fully processed molecules.
|
|
http://www.w3.org/1999/02/22-rdf-syntax-ns#type
|
http://www.w3.org/2002/07/owl#Class
|
|
http://www.geneontology.org/formats/oboInOwl#hasExactSynonym
|
mRNA features
|
|
http://www.w3.org/2000/01/rdf-schema#comment
|
This includes coding sequences for a signal or transit peptide. A signal peptide coding sequence encodes an N-terminal domain of a secreted protein, which is involved in attaching the polypeptide to a membrane leader sequence. A transit peptide coding sequence encodes an N-terminal domain of a nuclear-encoded organellar protein; which is involved in import of the protein into the organelle. |
| This includes regions or sites in a eukaryotic and eukaryotic viral RNA sequence which directs endonuclease cleavage or polyadenylation of an RNA transcript. A polyA signal is required for endonuclease cleavage of an RNA transcript that is followed by polyadenylation. A polyA site is a site on an RNA transcript to which adenine residues will be added during post-transcriptional polyadenylation. |
| This includes Introns, and protein-coding regions including coding sequences (CDS), exons, translation initiation sites and open reading frames. Also expressed sequence tag (EST) or complementary DNA (cDNA) sequences. |
| This includes 5'untranslated region (5'UTR), coding sequences (CDS), exons, intervening sequences (intron) and 3'untranslated regions (3'UTR).
|
|
http://www.w3.org/2000/01/rdf-schema#subClassOf
|
http://edamontology.org/topic_0099 |
| http://edamontology.org/topic_0114
|
|
http://www.geneontology.org/formats/oboInOwl#hasHumanReadableId
|
Gene_transcripts
|
http://edamontology.org/topic_3510 |
|
http://www.geneontology.org/formats/oboInOwl#inSubset
|
http://purl.obolibrary.org/obo/edam#topics |
| http://purl.obolibrary.org/obo/edam#edam
|
|
http://www.w3.org/2000/01/rdf-schema#label
|
Protein sites, features and motifs
|
|
http://edamontology.org/created_in
|
1.8
|
|
http://www.geneontology.org/formats/oboInOwl#hasNarrowSynonym
|
Protein sequence features |
| Signal peptide cleavage sites
|
|
http://www.geneontology.org/formats/oboInOwl#hasDefinition
|
The biology, archival, detection, prediction and analysis of positional features such as functional and other key sites, in protein sequences and the conserved patterns (motifs, profiles etc.) that may be used to describe them.
|
|
http://www.w3.org/1999/02/22-rdf-syntax-ns#type
|
http://www.w3.org/2002/07/owl#Class
|
|
http://www.w3.org/2000/01/rdf-schema#comment
|
A signal peptide coding sequence encodes an N-terminal domain of a secreted protein, which is involved in attaching the polypeptide to a membrane leader sequence. A transit peptide coding sequence encodes an N-terminal domain of a nuclear-encoded organellar protein; which is involved in import of the protein into the organelle.
|
|
http://www.w3.org/2000/01/rdf-schema#subClassOf
|
http://edamontology.org/topic_0160 |
| http://edamontology.org/topic_0078
|
|
http://www.geneontology.org/formats/oboInOwl#hasHumanReadableId
|
Protein_sites_features_and_motifs
|
http://edamontology.org/is_topic_of |
|
http://purl.obolibrary.org/obo/is_anti_symmetric
|
false
|
|
http://www.w3.org/2000/01/rdf-schema#label
|
is topic of
|
|
http://purl.obolibrary.org/obo/is_reflexive
|
false
|
|
http://www.geneontology.org/formats/oboInOwl#isCyclic
|
true
|
|
http://www.w3.org/2000/01/rdf-schema#range
|
_:379
|
|
http://www.geneontology.org/formats/oboInOwl#inSubset
|
edam |
| relations
|
|
http://purl.obolibrary.org/obo/is_symmetric
|
false
|
|
http://www.w3.org/2000/01/rdf-schema#domain
|
http://edamontology.org/topic_0003
|
|
http://www.w3.org/2000/01/rdf-schema#seeAlso
|
http://www.loa-cnr.it/ontologies/DOLCE-Lite.owl#inherent-in
|
|
http://www.geneontology.org/formats/oboInOwl#hasDefinition
|
'A is_topic_of B' defines for the subject A, that it is a topic of the object B (a topic A is the scope of B).
|
|
http://www.w3.org/1999/02/22-rdf-syntax-ns#type
|
http://www.w3.org/2002/07/owl#ObjectProperty
|
|
http://www.w3.org/2000/01/rdf-schema#comment
|
Subject A can either be a concept that is a 'Topic', or in unexpected cases an entity outside of an ontology (or an ontology concept in a role of an entity being semantically annotated) that is a 'Topic' or is in the role of a 'Topic'. Object B can be any concept or entity outside of an ontology. In EDAM, 'is_topic_of' is not explicitly defined between EDAM concepts, only the inverse 'has_topic'.
|
|
http://purl.obolibrary.org/obo/transitive_over
|
OBO_REL:is_a
|
|
http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym
|
OBO_REL:quality_of
|
http://edamontology.org/topic_3542 |
|
http://www.geneontology.org/formats/oboInOwl#inSubset
|
http://purl.obolibrary.org/obo/edam#topics |
| http://purl.obolibrary.org/obo/edam#edam
|
|
http://www.w3.org/2000/01/rdf-schema#label
|
Protein secondary structure
|
|
http://edamontology.org/created_in
|
1.8
|
|
http://www.geneontology.org/formats/oboInOwl#hasNarrowSynonym
|
Protein super-secondary structure
|
|
http://www.w3.org/2000/01/rdf-schema#seeAlso
|
https://en.wikipedia.org/wiki/Protein_secondary_structure
|
|
http://www.geneontology.org/formats/oboInOwl#hasDefinition
|
Secondary structure (predicted or real) of a protein, including super-secondary structure.
|
|
http://www.w3.org/1999/02/22-rdf-syntax-ns#type
|
http://www.w3.org/2002/07/owl#Class
|
|
http://www.geneontology.org/formats/oboInOwl#hasExactSynonym
|
Protein features (secondary structure)
|
|
http://www.w3.org/2000/01/rdf-schema#comment
|
The location and size of the secondary structure elements and intervening loop regions is typically given. The report can include disulphide bonds and post-translationally formed peptide bonds (crosslinks). |
| Super-secondary structures include leucine zippers, coiled coils, Helix-Turn-Helix etc.
|
|
http://www.geneontology.org/formats/oboInOwl#hasHumanReadableId
|
Protein_secondary_structure
|
|
http://www.w3.org/2000/01/rdf-schema#subClassOf
|
http://edamontology.org/topic_2814
|
http://edamontology.org/topic_3534 |
|
http://www.geneontology.org/formats/oboInOwl#inSubset
|
http://purl.obolibrary.org/obo/edam#topics |
| http://purl.obolibrary.org/obo/edam#edam
|
|
http://www.w3.org/2000/01/rdf-schema#label
|
Protein binding sites
|
|
http://edamontology.org/created_in
|
1.8
|
|
http://www.geneontology.org/formats/oboInOwl#hasNarrowSynonym
|
Enzyme active site |
| Protein-nucleic acid binding sites |
| Protein functional sites |
| Protein cleavage sites |
| Protein key folding sites
|
|
http://www.geneontology.org/formats/oboInOwl#hasDefinition
|
Binding sites in proteins, including cleavage sites (for a proteolytic enzyme or agent), key residues involved in protein folding, catalytic residues (active site) of an enzyme, ligand-binding (non-catalytic) residues of a protein, such as sites that bind metal, prosthetic groups or lipids, RNA and DNA-binding proteins and binding sites etc.
|
|
http://www.w3.org/1999/02/22-rdf-syntax-ns#type
|
http://www.w3.org/2002/07/owl#Class
|
|
http://www.geneontology.org/formats/oboInOwl#hasHumanReadableId
|
Protein_binding_sites
|
|
http://www.w3.org/2000/01/rdf-schema#subClassOf
|
http://edamontology.org/topic_3510
|
http://edamontology.org/is_identifier_of |
|
http://www.w3.org/2000/01/rdf-schema#range
|
http://edamontology.org/data_0006
|
|
http://www.geneontology.org/formats/oboInOwl#inSubset
|
edam |
| relations
|
|
http://purl.obolibrary.org/obo/is_anti_symmetric
|
false
|
|
http://www.w3.org/2000/01/rdf-schema#label
|
is identifier of
|
|
http://purl.obolibrary.org/obo/is_symmetric
|
false
|
|
http://www.w3.org/2000/01/rdf-schema#domain
|
http://edamontology.org/data_0842
|
|
http://www.geneontology.org/formats/oboInOwl#hasDefinition
|
'A is_identifier_of B' defines for the subject A, that it is an identifier of the object B.
|
|
http://www.w3.org/1999/02/22-rdf-syntax-ns#type
|
http://www.w3.org/2002/07/owl#ObjectProperty
|
|
http://purl.obolibrary.org/obo/is_reflexive
|
false
|
|
http://www.w3.org/2000/01/rdf-schema#comment
|
Subject A can either be a concept that is an 'Identifier', or an entity outside of an ontology (or an ontology concept in a role of an entity being semantically annotated) that is an 'Identifier' or is in the role of an 'Identifier'. Object B can be any concept or entity outside of an ontology. In EDAM, only 'is_identifier_of' is explicitly defined between EDAM concepts (only 'Identifier' 'is_identifier_of' 'Data'). The inverse, 'has_identifier', is not explicitly defined.
|
|
http://purl.obolibrary.org/obo/transitive_over
|
OBO_REL:is_a
|
|
http://www.geneontology.org/formats/oboInOwl#isCyclic
|
false
|
http://edamontology.org/operation_2495 |
|
http://www.geneontology.org/formats/oboInOwl#inSubset
|
http://purl.obolibrary.org/obo/edam#edam |
| http://purl.obolibrary.org/obo/edam#operations
|
|
http://www.geneontology.org/formats/oboInOwl#comment
|
Gene expression profiling generates some sort of gene expression profile, for example from microarray data. |
| Metagenomic inference is the profiling of phylogenetic marker genes in order to predict metagenome function. |
| The measurement of the gene expression of multiple genes in a cell, tissue, sample etc., in order to get an impression of biological function.
|
|
http://www.w3.org/2000/01/rdf-schema#label
|
Expression analysis
|
|
http://edamontology.org/created_in
|
beta12orEarlier
|
|
http://www.geneontology.org/formats/oboInOwl#hasNarrowSynonym
|
Metabolite expression analysis |
| Gene expression data analysis |
| Metagenomic inference |
| Gene expression profile construction |
| Non-coding RNA profiling |
| Protein profiling |
| Microarray data analysis |
| Gene transcription profiling |
| Gene expression quantification |
| Gene expression analysis |
| Functional profiling |
| RNA profiling |
| mRNA profiling |
| Protein expression analysis |
| Gene expression profiling |
| Gene expression profile generation
|
|
http://www.w3.org/2000/01/rdf-schema#seeAlso
|
https://en.wikipedia.org/wiki/Gene_expression_profiling |
| https://en.wikipedia.org/w/index.php?title=Gene_expression_analysis
|
|
http://www.geneontology.org/formats/oboInOwl#hasDefinition
|
Process (read and/or write) expression data from experiments measuring molecules (e.g. omics data), including analysis of one or more expression profiles, typically to interpret them in functional terms.
|
|
http://www.w3.org/1999/02/22-rdf-syntax-ns#type
|
http://www.w3.org/2002/07/owl#Class
|
|
http://www.geneontology.org/formats/oboInOwl#hasExactSynonym
|
Feature expression analysis |
| Expression data analysis
|
|
http://www.w3.org/2000/01/rdf-schema#subClassOf
|
_:424 |
| http://edamontology.org/operation_2945
|
http://edamontology.org/has_topic |
|
http://purl.obolibrary.org/obo/is_anti_symmetric
|
false
|
|
http://www.w3.org/2000/01/rdf-schema#label
|
has topic
|
|
http://purl.obolibrary.org/obo/is_reflexive
|
false
|
|
http://www.geneontology.org/formats/oboInOwl#isCyclic
|
true
|
|
http://www.geneontology.org/formats/oboInOwl#inSubset
|
edam |
| relations
|
|
http://www.w3.org/2000/01/rdf-schema#range
|
http://edamontology.org/topic_0003
|
|
http://purl.obolibrary.org/obo/is_symmetric
|
false
|
|
http://www.w3.org/2000/01/rdf-schema#domain
|
_:403
|
|
http://www.w3.org/2002/07/owl#inverseOf
|
http://edamontology.org/is_topic_of
|
|
http://www.w3.org/2000/01/rdf-schema#seeAlso
|
"http://purl.obolibrary.org/obo/IAO_0000136" |
| http://annotation-ontology.googlecode.com/svn/trunk/annotation-core.owl#hasTopic |
| http://www.loa-cnr.it/ontologies/DOLCE-Lite.owl#has-quality |
| "http://purl.obolibrary.org/obo/OBI_0000298"
|
|
http://www.geneontology.org/formats/oboInOwl#hasDefinition
|
'A has_topic B' defines for the subject A, that it has the object B as its topic (A is in the scope of a topic B).
|
|
http://www.w3.org/1999/02/22-rdf-syntax-ns#type
|
http://www.w3.org/2002/07/owl#ObjectProperty
|
|
http://www.w3.org/2000/01/rdf-schema#comment
|
Subject A can be any concept or entity outside of an ontology (or an ontology concept in a role of an entity being semantically annotated). Object B can either be a concept that is a 'Topic', or in unexpected cases an entity outside of an ontology that is a 'Topic' or is in the role of a 'Topic'. In EDAM, only 'has_topic' is explicitly defined between EDAM concepts ('Operation' or 'Data' 'has_topic' 'Topic'). The inverse, 'is_topic_of', is not explicitly defined.
|
|
http://purl.obolibrary.org/obo/transitive_over
|
OBO_REL:is_a
|
http://edamontology.org/data_2314 |
|
http://www.geneontology.org/formats/oboInOwl#inSubset
|
http://purl.obolibrary.org/obo/edam#edam |
| http://purl.obolibrary.org/obo/edam#data |
| http://purl.obolibrary.org/obo/edam#identifiers
|
|
http://www.w3.org/2000/01/rdf-schema#label
|
GI number
|
|
http://edamontology.org/created_in
|
beta12orEarlier
|
|
http://www.geneontology.org/formats/oboInOwl#hasDefinition
|
A series of digits that are assigned consecutively to each sequence record processed by NCBI. The GI number bears no resemblance to the Accession number of the sequence record.
|
|
http://www.w3.org/1999/02/22-rdf-syntax-ns#type
|
http://www.w3.org/2002/07/owl#Class
|
|
http://www.geneontology.org/formats/oboInOwl#hasExactSynonym
|
NCBI GI number
|
|
http://www.w3.org/2000/01/rdf-schema#comment
|
Nucleotide sequence GI number is shown in the VERSION field of the database record. Protein sequence GI number is shown in the CDS/db_xref field of a nucleotide database record, and the VERSION field of a protein database record.
|
|
http://www.w3.org/2000/01/rdf-schema#subClassOf
|
http://edamontology.org/data_2091 |
| http://edamontology.org/data_2362
|
http://edamontology.org/is_input_of |
|
http://purl.obolibrary.org/obo/is_anti_symmetric
|
false
|
|
http://www.w3.org/2000/01/rdf-schema#label
|
is input of
|
|
http://purl.obolibrary.org/obo/is_reflexive
|
false
|
|
http://www.geneontology.org/formats/oboInOwl#isCyclic
|
true
|
|
http://www.geneontology.org/formats/oboInOwl#inSubset
|
edam |
| relations
|
|
http://www.w3.org/2000/01/rdf-schema#range
|
http://edamontology.org/operation_0004
|
|
http://purl.obolibrary.org/obo/is_symmetric
|
false
|
|
http://www.w3.org/2000/01/rdf-schema#domain
|
http://edamontology.org/data_0006
|
|
http://www.w3.org/2000/01/rdf-schema#seeAlso
|
http://wsio.org/is_input_of |
| "http://purl.obolibrary.org/obo/OBI_0000295"
|
|
http://www.geneontology.org/formats/oboInOwl#hasDefinition
|
'A is_input_of B' defines for the subject A, that it as a necessary or actual input or input argument of the object B.
|
|
http://www.w3.org/1999/02/22-rdf-syntax-ns#type
|
http://www.w3.org/2002/07/owl#ObjectProperty
|
|
http://www.w3.org/2000/01/rdf-schema#comment
|
Subject A can be any concept or entity outside of an ontology (or an ontology concept in a role of an entity being semantically annotated). Object B can either be a concept that is or has an 'Operation' function, or an entity outside of an ontology that has an 'Operation' function or is an 'Operation'. In EDAM, 'is_input_of' is not explicitly defined between EDAM concepts, only the inverse 'has_input'.
|
|
http://purl.obolibrary.org/obo/transitive_over
|
OBO_REL:is_a
|
|
http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym
|
OBO_REL:participates_in
|
http://edamontology.org/is_function_of |
|
http://purl.obolibrary.org/obo/is_anti_symmetric
|
false
|
|
http://www.w3.org/2000/01/rdf-schema#label
|
is function of
|
|
http://purl.obolibrary.org/obo/is_reflexive
|
false
|
|
http://www.geneontology.org/formats/oboInOwl#isCyclic
|
true
|
|
http://www.geneontology.org/formats/oboInOwl#inSubset
|
edam |
| relations
|
|
http://purl.obolibrary.org/obo/is_symmetric
|
false
|
|
http://www.w3.org/2000/01/rdf-schema#domain
|
http://edamontology.org/operation_0004
|
|
http://www.geneontology.org/formats/oboInOwl#hasNarrowSynonym
|
OBO_REL:function_of
|
|
http://www.w3.org/2000/01/rdf-schema#seeAlso
|
http://www.loa-cnr.it/ontologies/DOLCE-Lite.owl#inherent-in |
| http://wsio.org/is_function_of
|
|
http://www.geneontology.org/formats/oboInOwl#hasDefinition
|
'A is_function_of B' defines for the subject A, that it is a function of the object B.
|
|
http://www.w3.org/1999/02/22-rdf-syntax-ns#type
|
http://www.w3.org/2002/07/owl#ObjectProperty
|
|
http://www.w3.org/2000/01/rdf-schema#comment
|
Subject A can either be concept that is (or is in a role of) a function, or an entity outside of an ontology (or an ontology concept in a role of an entity being semantically annotated) that is (or is in a role of) a function specification. Object B can be any concept or entity. Within EDAM itself, 'is_function_of' is not used.
|
|
http://purl.obolibrary.org/obo/transitive_over
|
OBO_REL:is_a
|
|
http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym
|
OBO_REL:inheres_in
|
http://edamontology.org/operation_2436 |
|
http://www.w3.org/2000/01/rdf-schema#label
|
Gene-set enrichment analysis
|
|
http://edamontology.org/created_in
|
beta12orEarlier
|
|
http://www.geneontology.org/formats/oboInOwl#hasExactSynonym
|
GSEA |
| Gene-set over-represenation analysis |
| Functional enrichment analysis
|
|
http://www.geneontology.org/formats/oboInOwl#inSubset
|
http://purl.obolibrary.org/obo/edam#edam |
| http://purl.obolibrary.org/obo/edam#operations
|
|
http://www.geneontology.org/formats/oboInOwl#comment
|
Gene sets can be defined beforehand by biological function, chromosome locations and so on. |
| Analyse gene expression patterns to identify sets of genes that are associated with a specific trait, condition, clinical outcome etc.
|
|
http://www.geneontology.org/formats/oboInOwl#hasNarrowSynonym
|
Gene set analysis
|
|
http://www.w3.org/2000/01/rdf-schema#seeAlso
|
https://en.wikipedia.org/wiki/Gene_Ontology_Term_Enrichment |
| https://en.wikipedia.org/wiki/Gene_set_enrichment_analysis
|
|
http://www.geneontology.org/formats/oboInOwl#hasDefinition
|
Identify classes of genes or proteins that are over or under-represented in a large set of genes or proteins. For example analysis of a set of genes corresponding to a gene expression profile, annotated with Gene Ontology (GO) concepts, where eventual over-/under-representation of certain GO concept within the studied set of genes is revealed.
|
|
http://www.w3.org/1999/02/22-rdf-syntax-ns#type
|
http://www.w3.org/2002/07/owl#Class
|
|
http://www.w3.org/2000/01/rdf-schema#comment
|
"Gene set analysis" (often used interchangeably or in an overlapping sense with "gene-set enrichment analysis") refers to the functional analysis (term enrichment) of a differentially expressed set of genes, rather than all genes analysed. |
| The Gene Ontology (GO) is typically used, the input is a set of Gene IDs, and the output of the analysis is typically a ranked list of GO concepts, each associated with a p-value.
|
|
http://www.w3.org/2000/01/rdf-schema#subClassOf
|
http://edamontology.org/operation_3501 |
| _:401 |
| http://edamontology.org/operation_2495 |
| _:487
|
|
http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym
|
Gene Ontology concept enrichment |
| GO-term enrichment |
| Gene Ontology term enrichment
|
|
http://www.geneontology.org/formats/oboInOwl#hasBroadSynonym
|
Gene set testing
|
http://edamontology.org/topic_0625 |
|
http://www.geneontology.org/formats/oboInOwl#inSubset
|
http://purl.obolibrary.org/obo/edam#events |
| http://purl.obolibrary.org/obo/edam#topics |
| http://purl.obolibrary.org/obo/edam#edam
|
|
http://edamontology.org/isdebtag
|
true
|
|
http://www.w3.org/2000/01/rdf-schema#label
|
Genotype and phenotype
|
|
http://edamontology.org/created_in
|
beta12orEarlier
|
|
http://www.geneontology.org/formats/oboInOwl#hasNarrowSynonym
|
Genotyping |
| Phenotyping |
| Genotype |
| Phenotype
|
|
http://www.w3.org/2000/01/rdf-schema#seeAlso
|
https://en.wikipedia.org/wiki/Genotype%E2%80%93phenotype_distinction
|
|
http://www.geneontology.org/formats/oboInOwl#hasDefinition
|
The study of genetic constitution of a living entity, such as an individual, and organism, a cell and so on, typically with respect to a particular observable phenotypic traits, or resources concerning such traits, which might be an aspect of biochemistry, physiology, morphology, anatomy, development and so on.
|
|
http://www.w3.org/1999/02/22-rdf-syntax-ns#type
|
http://www.w3.org/2002/07/owl#Class
|
|
http://www.geneontology.org/formats/oboInOwl#hasExactSynonym
|
Genotype-phenotype analysis |
| Genotype-phenotype |
| Genotype and phenotype resources
|
|
http://www.w3.org/2000/01/rdf-schema#subClassOf
|
http://edamontology.org/topic_3053
|
|
http://www.geneontology.org/formats/oboInOwl#hasHumanReadableId
|
Genotype_and_phenotype
|
http://edamontology.org/topic_0623 |
|
http://www.geneontology.org/formats/oboInOwl#inSubset
|
http://purl.obolibrary.org/obo/edam#events |
| http://purl.obolibrary.org/obo/edam#topics |
| http://purl.obolibrary.org/obo/edam#edam
|
|
http://edamontology.org/isdebtag
|
true
|
|
http://www.w3.org/2000/01/rdf-schema#label
|
Gene and protein families
|
|
http://edamontology.org/created_in
|
beta12orEarlier
|
|
http://www.geneontology.org/formats/oboInOwl#hasNarrowSynonym
|
Protein sequence classification |
| Gene family |
| Gene families |
| Protein families |
| Gene system
|
|
http://www.w3.org/2000/01/rdf-schema#seeAlso
|
https://en.wikipedia.org/wiki/Gene_family |
| https://en.wikipedia.org/wiki/Protein_family
|
|
http://www.geneontology.org/formats/oboInOwl#hasDefinition
|
Particular gene(s), gene family or other gene group or system and their encoded proteins.Primarily the classification of proteins (from sequence or structural data) into clusters, groups, families etc., curation of a particular protein or protein family, or any other proteins that have been classified as members of a common group.
|
|
http://www.w3.org/1999/02/22-rdf-syntax-ns#type
|
http://www.w3.org/2002/07/owl#Class
|
|
http://www.geneontology.org/formats/oboInOwl#hasExactSynonym
|
Genes, gene family or system
|
|
http://www.w3.org/2000/01/rdf-schema#comment
|
A protein families database might include the classifier (e.g. a sequence profile) used to build the classification.
|
|
http://www.w3.org/2000/01/rdf-schema#subClassOf
|
http://edamontology.org/topic_0078 |
| http://edamontology.org/topic_3321
|
|
http://www.geneontology.org/formats/oboInOwl#hasHumanReadableId
|
Gene_and protein_families
|
http://edamontology.org/topic_0602 |
|
http://www.geneontology.org/formats/oboInOwl#inSubset
|
http://purl.obolibrary.org/obo/edam#events |
| http://purl.obolibrary.org/obo/edam#topics |
| http://purl.obolibrary.org/obo/edam#edam
|
|
http://edamontology.org/isdebtag
|
true
|
|
http://www.w3.org/2000/01/rdf-schema#label
|
Molecular interactions, pathways and networks
|
|
http://edamontology.org/created_in
|
beta12orEarlier
|
|
http://www.geneontology.org/formats/oboInOwl#hasAlternativeId
|
http://edamontology.org/topic_3076
|
|
http://www.geneontology.org/formats/oboInOwl#hasNarrowSynonym
|
Signaling pathways |
| Biological pathways |
| Genetic information processing pathways |
| Molecular interactions |
| Pathways |
| Signal transduction pathways |
| Metabolic pathways |
| Biological networks |
| Interactome |
| Networks |
| Gene regulatory networks |
| Interactions |
| Cellular process pathways |
| Biological models |
| Environmental information processing pathways |
| Disease pathways
|
|
http://www.w3.org/2000/01/rdf-schema#seeAlso
|
https://en.wikipedia.org/wiki/Metabolic_pathway |
| https://en.wikipedia.org/wiki/Interactome
|
|
http://www.geneontology.org/formats/oboInOwl#hasDefinition
|
Molecular interactions, biological pathways, networks and other models.
|
|
http://www.w3.org/1999/02/22-rdf-syntax-ns#type
|
http://www.w3.org/2002/07/owl#Class
|
|
http://www.geneontology.org/formats/oboInOwl#hasHumanReadableId
|
Molecular_interactions_pathways_and_networks
|
|
http://www.w3.org/2000/01/rdf-schema#subClassOf
|
http://edamontology.org/topic_3307
|
http://edamontology.org/topic_0601 |
|
http://edamontology.org/isdebtag
|
true
|
|
http://www.w3.org/2000/01/rdf-schema#label
|
Protein modifications
|
|
http://edamontology.org/created_in
|
beta12orEarlier
|
|
http://www.geneontology.org/formats/oboInOwl#hasExactSynonym
|
Protein post-translational modification
|
|
http://www.geneontology.org/formats/oboInOwl#inSubset
|
http://purl.obolibrary.org/obo/edam#topics |
| http://purl.obolibrary.org/obo/edam#edam
|
|
http://www.geneontology.org/formats/oboInOwl#hasNarrowSynonym
|
Protein chemical modifications |
| Post-translation modifications |
| Protein post-translational modifications
|
|
http://www.w3.org/2000/01/rdf-schema#seeAlso
|
https://en.wikipedia.org/wiki/Post-translational_modification
|
|
http://www.geneontology.org/formats/oboInOwl#hasDefinition
|
Protein chemical modifications, e.g. post-translational modifications.
|
|
http://www.w3.org/1999/02/22-rdf-syntax-ns#type
|
http://www.w3.org/2002/07/owl#Class
|
|
http://www.w3.org/2000/01/rdf-schema#comment
|
EDAM does not describe all possible protein modifications. For fine-grained annotation of protein modification use the Gene Ontology (children of concept GO:0006464) and/or the Protein Modifications ontology (children of concept MOD:00000)
|
|
http://www.w3.org/2000/01/rdf-schema#subClassOf
|
http://edamontology.org/topic_0108
|
|
http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym
|
GO:0006464 |
| MOD:00000
|
|
http://www.geneontology.org/formats/oboInOwl#hasHumanReadableId
|
Protein_modifications
|
http://edamontology.org/operation_2454 |
|
http://www.geneontology.org/formats/oboInOwl#inSubset
|
http://purl.obolibrary.org/obo/edam#edam |
| http://purl.obolibrary.org/obo/edam#operations
|
|
http://www.geneontology.org/formats/oboInOwl#comment
|
Includes methods that predict whole gene structure using a combination of multiple methods to achieve better predictions.
|
|
http://www.w3.org/2000/01/rdf-schema#label
|
Gene prediction
|
|
http://edamontology.org/created_in
|
beta12orEarlier
|
|
http://www.geneontology.org/formats/oboInOwl#hasNarrowSynonym
|
Whole gene prediction
|
|
http://www.w3.org/2000/01/rdf-schema#seeAlso
|
https://en.wikipedia.org/wiki/Gene_prediction
|
|
http://www.geneontology.org/formats/oboInOwl#hasDefinition
|
Detect, predict and identify genes or components of genes in DNA sequences, including promoters, coding regions, splice sites, etc.
|
|
http://www.w3.org/1999/02/22-rdf-syntax-ns#type
|
http://www.w3.org/2002/07/owl#Class
|
|
http://www.geneontology.org/formats/oboInOwl#hasExactSynonym
|
Gene calling |
| Gene finding
|
|
http://www.w3.org/2000/01/rdf-schema#comment
|
Methods for gene prediction might be ab initio, based on phylogenetic comparisons, use motifs, sequence features, support vector machine, alignment etc.
|
|
http://www.w3.org/2000/01/rdf-schema#subClassOf
|
http://edamontology.org/operation_0415 |
| _:262 |
| _:307
|
http://edamontology.org/has_function |
|
http://purl.obolibrary.org/obo/is_anti_symmetric
|
false
|
|
http://www.w3.org/2000/01/rdf-schema#label
|
has function
|
|
http://purl.obolibrary.org/obo/is_reflexive
|
false
|
|
http://www.geneontology.org/formats/oboInOwl#isCyclic
|
true
|
|
http://www.geneontology.org/formats/oboInOwl#inSubset
|
edam |
| relations
|
|
http://www.w3.org/2000/01/rdf-schema#range
|
http://edamontology.org/operation_0004
|
|
http://purl.obolibrary.org/obo/is_symmetric
|
false
|
|
http://www.w3.org/2002/07/owl#inverseOf
|
http://edamontology.org/is_function_of
|
|
http://www.w3.org/2000/01/rdf-schema#seeAlso
|
http://wsio.org/has_function |
| "http://purl.obolibrary.org/obo/OBI_0000306" |
| http://www.loa-cnr.it/ontologies/DOLCE-Lite.owl#has-quality"
|
|
http://www.geneontology.org/formats/oboInOwl#hasDefinition
|
'A has_function B' defines for the subject A, that it has the object B as its function.
|
|
http://www.w3.org/1999/02/22-rdf-syntax-ns#type
|
http://www.w3.org/2002/07/owl#ObjectProperty
|
|
http://www.w3.org/2000/01/rdf-schema#comment
|
Subject A can be any concept or entity outside of an ontology (or an ontology concept in a role of an entity being semantically annotated). Object B can either be a concept that is (or is in a role of) a function, or an entity outside of an ontology that is (or is in a role of) a function specification. In the scope of EDAM, 'has_function' serves only for relating annotated entities outside of EDAM with 'Operation' concepts.
|
|
http://purl.obolibrary.org/obo/transitive_over
|
OBO_REL:is_a
|
|
http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym
|
OBO_REL:bearer_of
|
http://edamontology.org/topic_2885 |
|
http://www.geneontology.org/formats/oboInOwl#inSubset
|
http://purl.obolibrary.org/obo/edam#topics |
| http://purl.obolibrary.org/obo/edam#edam
|
|
http://edamontology.org/isdebtag
|
true
|
|
http://www.w3.org/2000/01/rdf-schema#label
|
DNA polymorphism
|
|
http://edamontology.org/created_in
|
beta12orEarlier
|
|
http://www.geneontology.org/formats/oboInOwl#hasNarrowSynonym
|
RFLP |
| SNP |
| VNTR |
| Microsatellites |
| Variable number of tandem repeat polymorphism |
| Single nucleotide polymorphism |
| snps
|
|
http://www.w3.org/2000/01/rdf-schema#seeAlso
|
https://en.wikipedia.org/wiki/Single-nucleotide_polymorphism
|
|
http://www.geneontology.org/formats/oboInOwl#hasDefinition
|
DNA polymorphism.
|
|
http://www.w3.org/1999/02/22-rdf-syntax-ns#type
|
http://www.w3.org/2002/07/owl#Class
|
|
http://www.w3.org/2000/01/rdf-schema#comment
|
Includes restriction fragment length polymorphisms (RFLP) in a DNA sequence. An RFLP is defined by the presence or absence of a specific restriction site of a bacterial restriction enzyme. |
| Includes variable number of tandem repeat (VNTR) polymorphism in a DNA sequence. VNTRs occur in non-coding regions of DNA and consists sub-sequence that is repeated a multiple (and varied) number of times. |
| Includes single nucleotide polymorphisms (SNP) and associated data, for example, the discovery and annotation of SNPs. A SNP is a DNA sequence variation where a single nucleotide differs between members of a species or paired chromosomes in an individual. |
| Includes microsatellite polymorphism in a DNA sequence. A microsatellite polymorphism is a very short subsequence that is repeated a variable number of times between individuals. These repeats consist of the nucleotides cytosine and adenosine.
|
|
http://www.w3.org/2000/01/rdf-schema#subClassOf
|
http://edamontology.org/topic_0199 |
| http://edamontology.org/topic_0654
|
|
http://www.geneontology.org/formats/oboInOwl#hasHumanReadableId
|
DNA_polymorphism
|
http://edamontology.org/is_format_of |
|
http://purl.obolibrary.org/obo/is_anti_symmetric
|
false
|
|
http://www.w3.org/2000/01/rdf-schema#label
|
is format of
|
|
http://purl.obolibrary.org/obo/is_reflexive
|
false
|
|
http://www.geneontology.org/formats/oboInOwl#isCyclic
|
false
|
|
http://www.geneontology.org/formats/oboInOwl#inSubset
|
edam |
| relations
|
|
http://www.w3.org/2000/01/rdf-schema#range
|
http://edamontology.org/data_0006
|
|
http://purl.obolibrary.org/obo/is_symmetric
|
false
|
|
http://www.w3.org/2000/01/rdf-schema#domain
|
http://edamontology.org/format_1915
|
|
http://www.w3.org/2000/01/rdf-schema#seeAlso
|
http://www.loa-cnr.it/ontologies/DOLCE-Lite.owl#inherent-in
|
|
http://www.geneontology.org/formats/oboInOwl#hasDefinition
|
'A is_format_of B' defines for the subject A, that it is a data format of the object B.
|
|
http://www.w3.org/1999/02/22-rdf-syntax-ns#type
|
http://www.w3.org/2002/07/owl#ObjectProperty
|
|
http://www.w3.org/2000/01/rdf-schema#comment
|
Subject A can either be a concept that is a 'Format', or in unexpected cases an entity outside of an ontology (or an ontology concept in a role of an entity being semantically annotated) that is a 'Format' or is in the role of a 'Format'. Object B can be any concept or entity outside of an ontology that is (or is in a role of) 'Data', or an input, output, input or output argument of an 'Operation'. In EDAM, only 'is_format_of' is explicitly defined between EDAM concepts ('Format' 'is_format_of' 'Data'). The inverse, 'has_format', is not explicitly defined.
|
|
http://purl.obolibrary.org/obo/transitive_over
|
OBO_REL:is_a
|
|
http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym
|
OBO_REL:quality_of
|
http://edamontology.org/topic_0203 |
|
http://www.geneontology.org/formats/oboInOwl#inSubset
|
http://purl.obolibrary.org/obo/edam#events |
| http://purl.obolibrary.org/obo/edam#topics |
| http://purl.obolibrary.org/obo/edam#edam
|
|
http://edamontology.org/isdebtag
|
true
|
|
http://www.w3.org/2000/01/rdf-schema#label
|
Gene expression
|
|
http://www.geneontology.org/formats/oboInOwl#hasAlternativeId
|
http://edamontology.org/topic_0197
|
|
http://edamontology.org/created_in
|
beta12orEarlier
|
|
http://www.geneontology.org/formats/oboInOwl#hasNarrowSynonym
|
Gene translation |
| Gene transcription |
| DNA microarrays |
| Transcription |
| Codon usage |
| Gene expression profiling
|
|
http://www.w3.org/2000/01/rdf-schema#seeAlso
|
http://purl.bioontology.org/ontology/MSH/D015870 |
| https://en.wikipedia.org/wiki/Gene_expression
|
|
http://www.geneontology.org/formats/oboInOwl#hasDefinition
|
The analysis of levels and patterns of synthesis of gene products (proteins and functional RNA) including interpretation in functional terms of gene expression data.
|
|
http://www.w3.org/1999/02/22-rdf-syntax-ns#type
|
http://www.w3.org/2002/07/owl#Class
|
|
http://www.w3.org/2000/01/rdf-schema#comment
|
This includes the study of codon usage in nucleotide sequence(s), genetic codes and so on. |
| Gene expression levels are analysed by identifying, quantifying or comparing mRNA transcripts, for example using microarrays, RNA-seq, northern blots, gene-indexed expression profiles etc.
|
|
http://www.w3.org/2000/01/rdf-schema#subClassOf
|
http://edamontology.org/topic_3321
|
|
http://www.geneontology.org/formats/oboInOwl#hasHumanReadableId
|
Gene_expression
|
http://edamontology.org/topic_3307 |
|
http://www.geneontology.org/formats/oboInOwl#inSubset
|
http://purl.obolibrary.org/obo/edam#events |
| http://purl.obolibrary.org/obo/edam#topics |
| http://purl.obolibrary.org/obo/edam#edam
|
|
http://www.geneontology.org/formats/oboInOwl#hasDbXref
|
VT 1.5.19 Mathematical biology |
| VT 1.5.26 Theoretical biology |
| VT 1.5.12 Computational biology
|
|
http://edamontology.org/isdebtag
|
true
|
|
http://www.w3.org/2000/01/rdf-schema#label
|
Computational biology
|
|
http://edamontology.org/created_in
|
1.3
|
|
http://www.geneontology.org/formats/oboInOwl#hasNarrowSynonym
|
Theoretical biology |
| Mathematical biology |
| Biomathematics
|
|
http://www.w3.org/2000/01/rdf-schema#seeAlso
|
https://en.wikipedia.org/wiki/Computational_biology
|
|
http://www.geneontology.org/formats/oboInOwl#hasDefinition
|
The development and application of theory, analytical methods, mathematical models and computational simulation of biological systems.
|
|
http://www.w3.org/1999/02/22-rdf-syntax-ns#type
|
http://www.w3.org/2002/07/owl#Class
|
|
http://www.w3.org/2000/01/rdf-schema#comment
|
This includes the modeling and treatment of biological processes and systems in mathematical terms (theoretical biology).
|
|
http://www.geneontology.org/formats/oboInOwl#hasHumanReadableId
|
Computational_biology
|
|
http://www.w3.org/2000/01/rdf-schema#subClassOf
|
http://edamontology.org/topic_0003
|
http://edamontology.org/topic_3314 |
|
http://www.geneontology.org/formats/oboInOwl#inSubset
|
http://purl.obolibrary.org/obo/edam#events |
| http://purl.obolibrary.org/obo/edam#topics |
| http://purl.obolibrary.org/obo/edam#edam
|
|
http://www.geneontology.org/formats/oboInOwl#hasDbXref
|
VT 1.7.5 Electrochemistry |
| VT 1.7.9 Physical chemistry |
| VT 1.7.6 Inorganic and nuclear chemistry |
| VT 1.7.3 Colloid chemistry |
| VT 1.7.7 Mathematical chemistry |
| VT 1.7.2 Chemistry |
| VT 1.7.8 Organic chemistry |
| VT 1.7 Chemical sciences
|
|
http://www.w3.org/2000/01/rdf-schema#label
|
Chemistry
|
|
http://edamontology.org/created_in
|
1.3
|
|
http://www.geneontology.org/formats/oboInOwl#hasNarrowSynonym
|
Organic chemistry |
| Physical chemistry |
| Mathematical chemistry |
| Nuclear chemistry |
| Inorganic chemistry
|
|
http://www.w3.org/2000/01/rdf-schema#seeAlso
|
https://en.wikipedia.org/wiki/Chemistry
|
|
http://www.geneontology.org/formats/oboInOwl#hasDefinition
|
The composition and properties of matter, reactions, and the use of reactions to create new substances.
|
|
http://www.w3.org/1999/02/22-rdf-syntax-ns#type
|
http://www.w3.org/2002/07/owl#Class
|
|
http://www.geneontology.org/formats/oboInOwl#hasHumanReadableId
|
Chemistry
|
|
http://www.w3.org/2000/01/rdf-schema#subClassOf
|
http://edamontology.org/topic_0003
|
|
http://www.geneontology.org/formats/oboInOwl#hasBroadSynonym
|
Chemical science |
| VT 1.7.10 Polymer science |
| Polymer science
|
http://edamontology.org/operation_2950 |
|
http://www.geneontology.org/formats/oboInOwl#inSubset
|
http://purl.obolibrary.org/obo/edam#edam |
| http://purl.obolibrary.org/obo/edam#operations
|
|
http://www.geneontology.org/formats/oboInOwl#hasDbXref
|
WHATIF:ShowDrugContacts |
| WHATIF: HETGroupNames |
| WHATIF:HasMetalContacts |
| WHATIF:HasNegativeIonContactsPlus |
| WHATIF:HasNegativeIonContacts |
| WHATIF:ShowDrugContactsShort |
| WHATIF:HasMetalContactsPlus |
| WHATIF:ShowLigandContacts |
| WHATIF:HasNucleicContacts |
| WHATIF:ShowProteiNucleicContacts
|
|
http://www.w3.org/2000/01/rdf-schema#label
|
Residue distance calculation
|
|
http://edamontology.org/created_in
|
beta12orEarlier
|
|
http://www.geneontology.org/formats/oboInOwl#hasNarrowSynonym
|
Residue contact calculation (residue-nucleic acid) |
| WHATIF:SymmetryContact |
| Residue contact calculation (residue-negative ion) |
| HET group detection |
| Residue contact calculation (residue-metal) |
| Residue contact calculation (residue-ligand)
|
|
http://www.geneontology.org/formats/oboInOwl#hasDefinition
|
Calculate contacts between residues, or between residues and other groups, in a protein structure, on the basis of distance calculations.
|
|
http://www.w3.org/1999/02/22-rdf-syntax-ns#type
|
http://www.w3.org/2002/07/owl#Class
|
|
http://www.w3.org/2000/01/rdf-schema#comment
|
This includes identifying HET groups, which usually correspond to ligands, lipids, but might also (not consistently) include groups that are attached to amino acids. Each HET group is supposed to have a unique three letter code and a unique name which might be given in the output. It can also include calculation of symmetry contacts, i.e. a contact between two atoms in different asymmetric unit.
|
|
http://www.w3.org/2000/01/rdf-schema#subClassOf
|
http://edamontology.org/operation_0248
|
http://edamontology.org/operation_0300 |
|
http://www.geneontology.org/formats/oboInOwl#inSubset
|
http://purl.obolibrary.org/obo/edam#edam |
| http://purl.obolibrary.org/obo/edam#operations
|
|
http://www.w3.org/2000/01/rdf-schema#label
|
Sequence profile alignment
|
|
http://edamontology.org/created_in
|
beta12orEarlier
|
|
http://www.geneontology.org/formats/oboInOwl#hasNarrowSynonym
|
Sequence-profile alignment |
| Sequence-to-profile alignment |
| Profile-profile alignment |
| Profile-to-profile alignment
|
|
http://www.geneontology.org/formats/oboInOwl#hasDefinition
|
Align molecular sequence(s) to sequence profile(s), or profiles to other profiles. A profile typically represents a sequence alignment.
|
|
http://www.w3.org/1999/02/22-rdf-syntax-ns#type
|
http://www.w3.org/2002/07/owl#Class
|
|
http://www.w3.org/2000/01/rdf-schema#comment
|
A sequence profile typically represents a sequence alignment. Methods might perform one-to-one, one-to-many or many-to-many comparisons.
|
|
http://www.w3.org/2000/01/rdf-schema#subClassOf
|
_:525 |
| _:340 |
| http://edamontology.org/operation_0292 |
| _:362
|
http://edamontology.org/operation_0303 |
|
http://www.geneontology.org/formats/oboInOwl#inSubset
|
http://purl.obolibrary.org/obo/edam#edam |
| http://purl.obolibrary.org/obo/edam#operations
|
|
http://www.w3.org/2000/01/rdf-schema#label
|
Fold recognition
|
|
http://edamontology.org/created_in
|
beta12orEarlier
|
|
http://www.geneontology.org/formats/oboInOwl#hasDefinition
|
Recognize (predict and identify) known protein structural domains or folds in protein sequence(s) which (typically) are not accompanied by any significant sequence similarity to know structures.
|
|
http://www.w3.org/1999/02/22-rdf-syntax-ns#type
|
http://www.w3.org/2002/07/owl#Class
|
|
http://www.geneontology.org/formats/oboInOwl#hasExactSynonym
|
Protein fold prediction |
| Protein domain prediction |
| Protein fold recognition |
| Domain prediction |
| Fold prediction
|
|
http://www.w3.org/2000/01/rdf-schema#comment
|
Methods use some type of mapping between sequence and fold, for example secondary structure prediction and alignment, profile comparison, sequence properties, homologous sequence search, kernel machines etc. Domains and folds might be taken from SCOP or CATH.
|
|
http://www.w3.org/2000/01/rdf-schema#subClassOf
|
http://edamontology.org/operation_2997 |
| http://edamontology.org/operation_2479 |
| http://edamontology.org/operation_2406 |
| http://edamontology.org/operation_2928 |
| http://edamontology.org/operation_3092
|
http://edamontology.org/operation_0304 |
|
http://www.geneontology.org/formats/oboInOwl#inSubset
|
http://purl.obolibrary.org/obo/edam#obsolete
|
|
http://www.w3.org/2002/07/owl#deprecated
|
true
|
|
http://www.w3.org/2000/01/rdf-schema#label
|
Metadata retrieval
|
|
http://edamontology.org/created_in
|
beta12orEarlier
|
|
http://www.geneontology.org/formats/oboInOwl#hasDefinition
|
Search for and retrieve data concerning or describing some core data, as distinct from the primary data that is being described.
|
|
http://edamontology.org/deprecation_comment
|
(jison)Too fine-grained, the operation (Data retrieval) hasn't changed, just what is retrieved.
|
|
http://www.w3.org/1999/02/22-rdf-syntax-ns#type
|
http://www.w3.org/2002/07/owl#Class
|
|
http://www.geneontology.org/formats/oboInOwl#replacedBy
|
http://edamontology.org/operation_2422
|
|
http://www.w3.org/2000/01/rdf-schema#comment
|
This includes documentation, general information and other metadata on entities such as databases, database entries and tools.
|
|
http://edamontology.org/oldParent
|
http://edamontology.org/operation_2422
|
|
http://www.w3.org/2000/01/rdf-schema#subClassOf
|
http://www.w3.org/2002/07/owl#DeprecatedClass
|
|
http://edamontology.org/obsolete_since
|
1.17
|
http://edamontology.org/operation_0308 |
|
http://www.geneontology.org/formats/oboInOwl#inSubset
|
http://purl.obolibrary.org/obo/edam#edam |
| http://purl.obolibrary.org/obo/edam#operations
|
|
http://www.w3.org/2000/01/rdf-schema#label
|
PCR primer design
|
|
http://edamontology.org/created_in
|
beta12orEarlier
|
|
http://www.geneontology.org/formats/oboInOwl#hasNarrowSynonym
|
PCR primer design (for genotyping polymorphisms) |
| Primer quality estimation |
| PCR primer design (for conserved primers) |
| PCR primer design (for gene transcription profiling) |
| PCR primer design (based on gene structure) |
| PCR primer design (for large scale sequencing) |
| PCR primer design (for methylation PCRs)
|
|
http://www.w3.org/2000/01/rdf-schema#seeAlso
|
https://en.wikipedia.org/wiki/Primer_(molecular_biology)#PCR_primer_design
|
|
http://www.geneontology.org/formats/oboInOwl#hasDefinition
|
Design or predict oligonucleotide primers for PCR and DNA amplification etc.
|
|
http://www.w3.org/1999/02/22-rdf-syntax-ns#type
|
http://www.w3.org/2002/07/owl#Class
|
|
http://www.geneontology.org/formats/oboInOwl#hasExactSynonym
|
PCR primer prediction |
| Primer design
|
|
http://www.w3.org/2000/01/rdf-schema#comment
|
This includes predicting primers based on gene structure, promoters, exon-exon junctions, predicting primers that are conserved across multiple genomes or species, primers for for gene transcription profiling, for genotyping polymorphisms, for example single nucleotide polymorphisms (SNPs), for large scale sequencing, or for methylation PCRs. |
| Primer design involves predicting or selecting primers that are specific to a provided PCR template. Primers can be designed with certain properties such as size of product desired, primer size etc. The output might be a minimal or overlapping primer set.
|
|
http://www.w3.org/2000/01/rdf-schema#subClassOf
|
_:286 |
| _:499 |
| _:527 |
| http://edamontology.org/operation_2419
|
http://edamontology.org/operation_2938 |
|
http://www.geneontology.org/formats/oboInOwl#inSubset
|
http://purl.obolibrary.org/obo/edam#edam |
| http://purl.obolibrary.org/obo/edam#operations
|
|
http://www.w3.org/2000/01/rdf-schema#label
|
Dendrogram visualisation
|
|
http://edamontology.org/created_in
|
beta12orEarlier
|
|
http://www.geneontology.org/formats/oboInOwl#hasNarrowSynonym
|
Microarray checks view rendering |
| Microarray matrix tree plot rendering |
| Microarray tree or dendrogram rendering |
| Microarray 2-way dendrogram rendering
|
|
http://www.w3.org/2000/01/rdf-schema#seeAlso
|
https://en.wikipedia.org/wiki/Dendrogram
|
|
http://www.geneontology.org/formats/oboInOwl#hasDefinition
|
Visualise clustered expression data using a tree diagram.
|
|
http://www.w3.org/1999/02/22-rdf-syntax-ns#type
|
http://www.w3.org/2002/07/owl#Class
|
|
http://www.geneontology.org/formats/oboInOwl#hasExactSynonym
|
Expression data tree or dendrogram rendering |
| Dendrograph plotting |
| Expression data tree visualisation |
| Dendrograph visualisation |
| Dendrogram plotting
|
|
http://www.w3.org/2000/01/rdf-schema#subClassOf
|
http://edamontology.org/operation_0571
|
http://edamontology.org/operation_2949 |
|
http://www.geneontology.org/formats/oboInOwl#inSubset
|
http://purl.obolibrary.org/obo/edam#edam |
| http://purl.obolibrary.org/obo/edam#operations
|
|
http://www.geneontology.org/formats/oboInOwl#comment
|
Includes analysis of raw experimental protein-protein interaction data from for example yeast two-hybrid analysis, protein microarrays, immunoaffinity chromatography followed by mass spectrometry, phage display etc.
|
|
http://www.w3.org/2000/01/rdf-schema#label
|
Protein-protein interaction analysis
|
|
http://edamontology.org/created_in
|
beta12orEarlier
|
|
http://www.geneontology.org/formats/oboInOwl#hasNarrowSynonym
|
Protein interaction simulation |
| Protein interaction raw data analysis
|
|
http://www.geneontology.org/formats/oboInOwl#hasDefinition
|
Analyse the interactions of proteins with other proteins.
|
|
http://www.w3.org/1999/02/22-rdf-syntax-ns#type
|
http://www.w3.org/2002/07/owl#Class
|
|
http://www.geneontology.org/formats/oboInOwl#hasExactSynonym
|
Protein interaction analysis
|
|
http://www.w3.org/2000/01/rdf-schema#subClassOf
|
_:410 |
| http://edamontology.org/operation_1777 |
| _:358
|
http://edamontology.org/operation_0331 |
|
http://www.geneontology.org/formats/oboInOwl#inSubset
|
http://purl.obolibrary.org/obo/edam#edam |
| http://purl.obolibrary.org/obo/edam#operations
|
|
http://www.w3.org/2000/01/rdf-schema#label
|
Variant effect prediction
|
|
http://edamontology.org/created_in
|
beta12orEarlier
|
|
http://www.geneontology.org/formats/oboInOwl#hasNarrowSynonym
|
Protein SNP mapping |
| Protein mutation modelling |
| Protein stability change prediction
|
|
http://www.geneontology.org/formats/oboInOwl#hasDefinition
|
Predict the effect of point mutation on a protein structure, in terms of strucural effects and protein folding, stability and function.
|
|
http://www.w3.org/1999/02/22-rdf-syntax-ns#type
|
http://www.w3.org/2002/07/owl#Class
|
|
http://www.geneontology.org/formats/oboInOwl#hasExactSynonym
|
Variant functional prediction
|
|
http://www.w3.org/2000/01/rdf-schema#comment
|
Protein SNP mapping maps and modesl the effects of single nucleotide polymorphisms (SNPs) on protein structure(s). Methods might predict silent or pathological mutations.
|
|
http://www.w3.org/2000/01/rdf-schema#subClassOf
|
_:531 |
| http://edamontology.org/operation_2423 |
| _:532
|
http://edamontology.org/operation_0310 |
|
http://www.geneontology.org/formats/oboInOwl#inSubset
|
http://purl.obolibrary.org/obo/edam#edam |
| http://purl.obolibrary.org/obo/edam#operations
|
|
http://www.w3.org/2000/01/rdf-schema#label
|
Sequence assembly
|
|
http://edamontology.org/created_in
|
beta12orEarlier
|
|
http://www.geneontology.org/formats/oboInOwl#hasNarrowSynonym
|
Sequence assembly editing |
| Metagenomic assembly
|
|
http://www.geneontology.org/formats/oboInOwl#hasDefinition
|
Combine (align and merge) overlapping fragments of a DNA sequence to reconstruct the original sequence.
|
|
http://www.w3.org/1999/02/22-rdf-syntax-ns#type
|
http://www.w3.org/2002/07/owl#Class
|
|
http://www.w3.org/2000/01/rdf-schema#comment
|
For example, assemble overlapping reads from paired-end sequencers into contigs (a contiguous sequence corresponding to read overlaps). Or assemble contigs, for example ESTs and genomic DNA fragments, depending on the detected fragment overlaps.
|
|
http://www.w3.org/2000/01/rdf-schema#subClassOf
|
http://edamontology.org/operation_2403 |
| _:449 |
| http://edamontology.org/operation_2478 |
| _:536
|
http://edamontology.org/operation_0321 |
|
http://www.geneontology.org/formats/oboInOwl#inSubset
|
http://purl.obolibrary.org/obo/edam#edam |
| http://purl.obolibrary.org/obo/edam#operations
|
|
http://www.geneontology.org/formats/oboInOwl#hasDbXref
|
WHATIF: CorrectedPDBasXML |
| WHATIF: UseResidueDB |
| WHATIF: UseFileDB
|
|
http://www.w3.org/2000/01/rdf-schema#label
|
Protein structure validation
|
|
http://edamontology.org/created_in
|
beta12orEarlier
|
|
http://www.geneontology.org/formats/oboInOwl#hasNarrowSynonym
|
Residue validation
|
|
http://www.w3.org/2000/01/rdf-schema#seeAlso
|
https://en.wikipedia.org/wiki/Structure_validation
|
|
http://www.geneontology.org/formats/oboInOwl#hasDefinition
|
Evaluate the quality or correctness a protein three-dimensional model.
|
|
http://www.w3.org/1999/02/22-rdf-syntax-ns#type
|
http://www.w3.org/2002/07/owl#Class
|
|
http://www.geneontology.org/formats/oboInOwl#hasExactSynonym
|
Protein model validation
|
|
http://www.w3.org/2000/01/rdf-schema#comment
|
The PDB file format has had difficulties, inconsistencies and errors. Corrections can include identifying a meaningful sequence, removal of alternate atoms, correction of nomenclature problems, removal of incomplete residues and spurious waters, addition or removal of water, modelling of missing side chains, optimisation of cysteine bonds, regularisation of bond lengths, bond angles and planarities etc. |
| Model validation might involve checks for atomic packing, steric clashes (bumps), volume irregularities, agreement with electron density maps, number of amino acid residues, percentage of residues with missing or bad atoms, irregular Ramachandran Z-scores, irregular Chi-1 / Chi-2 normality scores, RMS-Z score on bonds and angles etc. |
| This includes methods that calculate poor quality residues. The scoring function to identify poor quality residues may consider residues with bad atoms or atoms with high B-factor, residues in the N- or C-terminal position, adjacent to an unstructured residue, non-canonical residues, glycine and proline (or adjacent to these such residues).
|
|
http://www.w3.org/2000/01/rdf-schema#subClassOf
|
_:493 |
| http://edamontology.org/operation_2428 |
| http://edamontology.org/operation_2406 |
| _:341
|
http://edamontology.org/operation_0387 |
|
http://www.geneontology.org/formats/oboInOwl#inSubset
|
http://purl.obolibrary.org/obo/edam#edam |
| http://purl.obolibrary.org/obo/edam#operations
|
|
http://www.geneontology.org/formats/oboInOwl#hasDbXref
|
WHATIF:ResidueAccessibilityVacuum |
| WHATIF:AtomAccessibilityMolecularPlus |
| WHATIF:AtomAccessibilityMolecular |
| WHATIF:ResidueAccessibilityVacuumMolecular |
| WHATIF:ResidueAccessibilitySolvent |
| WHATIF:TotAccessibilitySolvent |
| WHATIF:ResidueAccessibilityMolecular |
| WHATIF:TotAccessibilityMolecular
|
|
http://www.w3.org/2000/01/rdf-schema#label
|
Molecular surface calculation
|
|
http://edamontology.org/created_in
|
beta12orEarlier
|
|
http://www.geneontology.org/formats/oboInOwl#hasNarrowSynonym
|
Protein surface calculation |
| Protein residue surface calculation |
| Protein surface and interior calculation |
| Protein atom surface calculation
|
|
http://www.geneontology.org/formats/oboInOwl#hasDefinition
|
Calculate the molecular surface area in proteins and other macromolecules.
|
|
http://www.w3.org/1999/02/22-rdf-syntax-ns#type
|
http://www.w3.org/2002/07/owl#Class
|
|
http://www.w3.org/2000/01/rdf-schema#subClassOf
|
http://edamontology.org/operation_3351
|
http://edamontology.org/operation_3457 |
|
http://www.geneontology.org/formats/oboInOwl#inSubset
|
http://purl.obolibrary.org/obo/edam#edam |
| http://purl.obolibrary.org/obo/edam#operations
|
|
http://www.w3.org/2000/01/rdf-schema#label
|
Single particle analysis
|
|
http://edamontology.org/created_in
|
1.7
|
|
http://www.w3.org/2000/01/rdf-schema#seeAlso
|
https://en.wikipedia.org/wiki/Single_particle_analysis
|
|
http://www.geneontology.org/formats/oboInOwl#hasDefinition
|
An image processing technique that combines and analyze multiple images of a particulate sample, in order to produce an image with clearer features that are more easily interpreted.
|
|
http://www.w3.org/1999/02/22-rdf-syntax-ns#type
|
http://www.w3.org/2002/07/owl#Class
|
|
http://www.w3.org/2000/01/rdf-schema#comment
|
Single particle analysis is used to improve the information that can be obtained by relatively low resolution techniques, , e.g. an image of a protein or virus from transmission electron microscopy (TEM).
|
|
http://www.w3.org/2000/01/rdf-schema#subClassOf
|
http://edamontology.org/operation_3443 |
| _:547 |
| http://edamontology.org/operation_2480
|
http://edamontology.org/operation_3435 |
|
http://www.geneontology.org/formats/oboInOwl#inSubset
|
http://purl.obolibrary.org/obo/edam#edam |
| http://purl.obolibrary.org/obo/edam#operations
|
|
http://www.w3.org/2000/01/rdf-schema#label
|
Standardisation and normalisation
|
|
http://edamontology.org/created_in
|
1.6
|
|
http://www.geneontology.org/formats/oboInOwl#hasNarrowSynonym
|
Normalisation |
| Standardisation
|
|
http://www.geneontology.org/formats/oboInOwl#hasDefinition
|
Standardize or normalize data by some statistical method.
|
|
http://www.w3.org/1999/02/22-rdf-syntax-ns#type
|
http://www.w3.org/2002/07/owl#Class
|
|
http://www.w3.org/2000/01/rdf-schema#comment
|
In the simplest normalisation means adjusting values measured on different scales to a common scale (often between 0.0 and 1.0), but can refer to more sophisticated adjustment whereby entire probability distributions of adjusted values are brought into alignment. Standardisation typically refers to an operation whereby a range of values are standardised to measure how many standard deviations a value is from its mean.
|
|
http://www.w3.org/2000/01/rdf-schema#subClassOf
|
http://edamontology.org/operation_2238
|
http://edamontology.org/operation_0415 |
|
http://www.geneontology.org/formats/oboInOwl#inSubset
|
http://purl.obolibrary.org/obo/edam#edam |
| http://purl.obolibrary.org/obo/edam#operations
|
|
http://www.w3.org/2000/01/rdf-schema#label
|
Nucleic acid feature detection
|
|
http://edamontology.org/created_in
|
beta12orEarlier
|
|
http://www.geneontology.org/formats/oboInOwl#hasNarrowSynonym
|
Nucleic acid feature prediction |
| Nucleic acid site recognition |
| Nucleic acid feature recognition |
| Nucleic acid site detection |
| Nucleic acid site prediction
|
|
http://www.geneontology.org/formats/oboInOwl#hasDefinition
|
Predict, recognise and identify features in nucleotide sequences such as functional sites or regions, typically by scanning for known motifs, patterns and regular expressions.
|
|
http://www.w3.org/1999/02/22-rdf-syntax-ns#type
|
http://www.w3.org/2002/07/owl#Class
|
|
http://www.geneontology.org/formats/oboInOwl#hasExactSynonym
|
Sequence feature detection (nucleic acid)
|
|
http://www.w3.org/2000/01/rdf-schema#comment
|
Methods typically involve scanning for known motifs, patterns and regular expressions.
|
|
http://www.w3.org/2000/01/rdf-schema#subClassOf
|
_:565 |
| _:295 |
| http://edamontology.org/operation_2423 |
| http://edamontology.org/operation_2478
|
http://edamontology.org/operation_0420 |
|
http://www.geneontology.org/formats/oboInOwl#inSubset
|
http://purl.obolibrary.org/obo/edam#edam |
| http://purl.obolibrary.org/obo/edam#operations
|
|
http://www.w3.org/2000/01/rdf-schema#label
|
Nucleic acids-binding site prediction
|
|
http://edamontology.org/created_in
|
beta12orEarlier
|
|
http://www.geneontology.org/formats/oboInOwl#hasNarrowSynonym
|
Zinc finger prediction
|
|
http://www.geneontology.org/formats/oboInOwl#hasDefinition
|
Predict or detect RNA and DNA-binding binding sites in protein sequences.
|
|
http://www.w3.org/1999/02/22-rdf-syntax-ns#type
|
http://www.w3.org/2002/07/owl#Class
|
|
http://www.geneontology.org/formats/oboInOwl#hasExactSynonym
|
Protein-nucleic acid binding site prediction |
| Protein-nucleic acid binding site detection |
| Protein-nucleic acid binding prediction |
| Protein-nucleic acid binding detection
|
|
http://www.w3.org/2000/01/rdf-schema#comment
|
This includes methods that predict and optimise zinc finger protein domains for DNA/RNA binding (for example for transcription factors and nucleases).
|
|
http://www.w3.org/2000/01/rdf-schema#subClassOf
|
http://edamontology.org/operation_2575
|
http://edamontology.org/data_2975 |
|
http://www.geneontology.org/formats/oboInOwl#inSubset
|
http://purl.obolibrary.org/obo/edam#obsolete
|
|
http://www.w3.org/2002/07/owl#deprecated
|
true
|
|
http://www.w3.org/2000/01/rdf-schema#label
|
Nucleic acid sequence (raw)
|
|
http://edamontology.org/created_in
|
beta12orEarlier
|
|
http://www.geneontology.org/formats/oboInOwl#hasDefinition
|
A raw nucleic acid sequence.
|
|
http://edamontology.org/deprecation_comment
|
Deprecated because this is bloat / confusing & better handled as an EDAM Format concept - "raw" sequences just imply a particular format (i.e. one with a vanilla string, possible in a particular alphabet, with no metadata).
|
|
http://www.w3.org/1999/02/22-rdf-syntax-ns#type
|
http://www.w3.org/2002/07/owl#Class
|
|
http://www.geneontology.org/formats/oboInOwl#hasExactSynonym
|
Nucleic acid raw sequence |
| Raw sequence (nucleic acid) |
| Raw nucleic acid sequence |
| Nucleotide sequence (raw)
|
|
http://www.geneontology.org/formats/oboInOwl#replacedBy
|
http://edamontology.org/data_2977
|
|
http://edamontology.org/oldParent
|
http://edamontology.org/data_0848
|
|
http://www.w3.org/2000/01/rdf-schema#subClassOf
|
http://www.w3.org/2002/07/owl#DeprecatedClass
|
|
http://edamontology.org/obsolete_since
|
1.23
|
http://edamontology.org/topic_3489 |
|
http://www.geneontology.org/formats/oboInOwl#inSubset
|
http://purl.obolibrary.org/obo/edam#topics |
| http://purl.obolibrary.org/obo/edam#edam
|
|
http://www.w3.org/2000/01/rdf-schema#label
|
Database management
|
|
http://edamontology.org/created_in
|
1.8
|
|
http://www.geneontology.org/formats/oboInOwl#hasNarrowSynonym
|
Content management |
| Data maintenance |
| Document, record and content management |
| Document management |
| Biological databases |
| File management |
| Record management
|
|
http://www.w3.org/2000/01/rdf-schema#seeAlso
|
https://en.wikipedia.org/wiki/Database
|
|
http://www.geneontology.org/formats/oboInOwl#hasDefinition
|
The general handling of data stored in digital archives such as databanks, databases proper, web portals and other data resources.
|
|
http://www.w3.org/1999/02/22-rdf-syntax-ns#type
|
http://www.w3.org/2002/07/owl#Class
|
|
http://www.geneontology.org/formats/oboInOwl#hasExactSynonym
|
Database administration |
| Databases
|
|
http://www.w3.org/2000/01/rdf-schema#comment
|
This includes databases for the results of scientific experiments, the application of high-throughput technology, computational analysis and the scientific literature. It covers the management and manipulation of digital documents, including database records, files and reports.
|
|
http://www.w3.org/2000/01/rdf-schema#subClassOf
|
http://edamontology.org/topic_3071
|
|
http://www.geneontology.org/formats/oboInOwl#hasHumanReadableId
|
Database_management
|
http://edamontology.org/operation_0438 |
|
http://www.geneontology.org/formats/oboInOwl#inSubset
|
http://purl.obolibrary.org/obo/edam#edam |
| http://purl.obolibrary.org/obo/edam#operations
|
|
http://www.geneontology.org/formats/oboInOwl#comment
|
This includes comparative genomics approaches that identify common, conserved (homologous) or synonymous transcriptional regulatory elements. For example cross-species comparison of transcription factor binding sites (TFBS). Methods might analyse co-regulated or co-expressed genes, or sets of oppositely expressed genes.
|
|
http://www.w3.org/2000/01/rdf-schema#label
|
Transcriptional regulatory element prediction
|
|
http://edamontology.org/created_in
|
beta12orEarlier
|
|
http://www.geneontology.org/formats/oboInOwl#hasNarrowSynonym
|
Conserved transcription regulatory sequence identification |
| Translational regulatory element prediction
|
|
http://www.geneontology.org/formats/oboInOwl#hasDefinition
|
Identify or predict transcriptional regulatory motifs, patterns, elements or regions in DNA sequences.
|
|
http://www.w3.org/1999/02/22-rdf-syntax-ns#type
|
http://www.w3.org/2002/07/owl#Class
|
|
http://www.geneontology.org/formats/oboInOwl#hasExactSynonym
|
Transcription regulatory element prediction |
| Regulatory element prediction
|
|
http://www.w3.org/2000/01/rdf-schema#comment
|
This includes promoters, enhancers, silencers and boundary elements / insulators, regulatory protein or transcription factor binding sites etc. Methods might be specific to a particular genome and use motifs, word-based / grammatical methods, position-specific frequency matrices, discriminative pattern analysis etc.
|
|
http://www.w3.org/2000/01/rdf-schema#subClassOf
|
http://edamontology.org/operation_2454 |
| _:414
|
http://edamontology.org/format_3590 |
|
http://www.geneontology.org/formats/oboInOwl#inSubset
|
http://purl.obolibrary.org/obo/edam#formats |
| http://purl.obolibrary.org/obo/edam#edam
|
|
http://www.geneontology.org/formats/oboInOwl#hasDbXref
|
https://www.hdfgroup.org/HDF5/doc/H5.format.html
|
|
http://www.w3.org/2000/01/rdf-schema#label
|
HDF5
|
|
http://edamontology.org/created_in
|
1.11
|
|
http://www.geneontology.org/formats/oboInOwl#hasDefinition
|
HDF5 is a data model, library, and file format for storing and managing data, based on Hierarchical Data Format (HDF).
|
|
http://edamontology.org/documentation
|
https://www.hdfgroup.org/HDF5/doc/H5.format.html
|
|
http://www.w3.org/1999/02/22-rdf-syntax-ns#type
|
http://www.w3.org/2002/07/owl#Class
|
|
http://www.geneontology.org/formats/oboInOwl#hasExactSynonym
|
h5
|
|
http://www.w3.org/2000/01/rdf-schema#comment
|
HDF5 is the new version, according to the HDF group, a completely different technology (https://support.hdfgroup.org/products/hdf4/ compared to HDF. |
| An HDF5 file appears to the user as a directed graph. The nodes of this graph are the higher-level HDF5 objects that are exposed by the HDF5 APIs: Groups, Datasets, Named datatypes. Currently supported by the Python MDTraj package.
|
|
http://www.w3.org/2000/01/rdf-schema#subClassOf
|
http://edamontology.org/format_3867 |
| http://edamontology.org/format_2333
|
http://edamontology.org/operation_0441 |
|
http://www.geneontology.org/formats/oboInOwl#inSubset
|
http://purl.obolibrary.org/obo/edam#edam |
| http://purl.obolibrary.org/obo/edam#operations
|
|
http://www.w3.org/2000/01/rdf-schema#label
|
cis-regulatory element prediction
|
|
http://edamontology.org/created_in
|
beta12orEarlier
|
|
http://www.geneontology.org/formats/oboInOwl#hasNarrowSynonym
|
Transcriptional regulatory element prediction (DNA-cis) |
| Transcriptional regulatory element prediction (RNA-cis)
|
|
http://www.geneontology.org/formats/oboInOwl#hasDefinition
|
Identify, predict or analyse cis-regulatory elements in DNA sequences (TATA box, Pribnow box, SOS box, CAAT box, CCAAT box, operator etc.) or in RNA sequences (e.g. riboswitches).
|
|
http://www.w3.org/1999/02/22-rdf-syntax-ns#type
|
http://www.w3.org/2002/07/owl#Class
|
|
http://www.w3.org/2000/01/rdf-schema#comment
|
Cis-regulatory elements (cis-elements) regulate the expression of genes located on the same strand from which the element was transcribed. Cis-elements are found in the 5' promoter region of the gene, in an intron, or in the 3' untranslated region. Cis-elements are often binding sites of one or more trans-acting factors. They also occur in RNA sequences, e.g. a riboswitch is a region of an mRNA molecule that bind a small target molecule that regulates the gene's activity.
|
|
http://www.w3.org/2000/01/rdf-schema#subClassOf
|
http://edamontology.org/operation_0438
|
http://edamontology.org/operation_3501 |
|
http://www.geneontology.org/formats/oboInOwl#inSubset
|
http://purl.obolibrary.org/obo/edam#edam |
| http://purl.obolibrary.org/obo/edam#operations
|
|
http://www.w3.org/2000/01/rdf-schema#label
|
Enrichment analysis
|
|
http://edamontology.org/created_in
|
1.8
|
|
http://www.geneontology.org/formats/oboInOwl#hasNarrowSynonym
|
Functional enrichment
|
|
http://www.geneontology.org/formats/oboInOwl#hasDefinition
|
Analysis of a set of objects, such as genes, annotated with given categories, where eventual over-/under-representation of certain categories within the studied set of objects is revealed.
|
|
http://www.w3.org/1999/02/22-rdf-syntax-ns#type
|
http://www.w3.org/2002/07/owl#Class
|
|
http://www.geneontology.org/formats/oboInOwl#hasExactSynonym
|
Enrichment |
| Over-representation analysis
|
|
http://www.w3.org/2000/01/rdf-schema#comment
|
Categories from a relevant ontology can be used. The input is typically a set of genes or other biological objects, possibly represented by their identifiers, and the output of the analysis is typically a ranked list of categories, each associated with a statistical metric of over-/under-representation within the studied data.
|
|
http://www.w3.org/2000/01/rdf-schema#subClassOf
|
http://edamontology.org/operation_2945 |
| _:319
|
http://edamontology.org/operation_0477 |
|
http://www.geneontology.org/formats/oboInOwl#inSubset
|
http://purl.obolibrary.org/obo/edam#edam |
| http://purl.obolibrary.org/obo/edam#operations
|
|
http://www.w3.org/2000/01/rdf-schema#label
|
Protein modelling
|
|
http://edamontology.org/created_in
|
beta12orEarlier
|
|
http://www.w3.org/2000/01/rdf-schema#seeAlso
|
https://en.wikipedia.org/wiki/Homology_modeling
|
|
http://www.geneontology.org/formats/oboInOwl#hasDefinition
|
Build a three-dimensional protein model based on known (for example homologs) structures.
|
|
http://www.w3.org/1999/02/22-rdf-syntax-ns#type
|
http://www.w3.org/2002/07/owl#Class
|
|
http://www.geneontology.org/formats/oboInOwl#hasExactSynonym
|
Homology structure modelling |
| Comparative modelling |
| Protein structure comparative modelling |
| Homology modelling
|
|
http://www.w3.org/2000/01/rdf-schema#comment
|
The model might be of a whole, part or aspect of protein structure. Molecular modelling methods might use sequence-structure alignment, structural templates, molecular dynamics, energy minimisation etc.
|
|
http://www.w3.org/2000/01/rdf-schema#subClassOf
|
_:405 |
| http://edamontology.org/operation_0474 |
| http://edamontology.org/operation_2426
|
http://edamontology.org/operation_0478 |
|
http://www.geneontology.org/formats/oboInOwl#inSubset
|
http://purl.obolibrary.org/obo/edam#edam |
| http://purl.obolibrary.org/obo/edam#operations
|
|
http://www.w3.org/2000/01/rdf-schema#label
|
Molecular docking
|
|
http://edamontology.org/created_in
|
beta12orEarlier
|
|
http://www.w3.org/2000/01/rdf-schema#seeAlso
|
https://en.wikipedia.org/wiki/Docking_(molecular) |
| https://en.wikipedia.org/wiki/Macromolecular_docking
|
|
http://www.geneontology.org/formats/oboInOwl#hasDefinition
|
Model the structure of a protein in complex with a small molecule or another macromolecule.
|
|
http://www.w3.org/1999/02/22-rdf-syntax-ns#type
|
http://www.w3.org/2002/07/owl#Class
|
|
http://www.geneontology.org/formats/oboInOwl#hasExactSynonym
|
Macromolecular docking |
| Docking simulation
|
|
http://www.w3.org/2000/01/rdf-schema#comment
|
This includes protein-protein interactions, protein-nucleic acid, protein-ligand binding etc. Methods might predict whether the molecules are likely to bind in vivo, their conformation when bound, the strength of the interaction, possible mutations to achieve bonding and so on.
|
|
http://www.w3.org/2000/01/rdf-schema#subClassOf
|
_:371 |
| _:573 |
| http://edamontology.org/operation_1777 |
| http://edamontology.org/operation_2480
|
http://edamontology.org/operation_0484 |
|
http://www.geneontology.org/formats/oboInOwl#inSubset
|
http://purl.obolibrary.org/obo/edam#edam |
| http://purl.obolibrary.org/obo/edam#operations
|
|
http://www.w3.org/2000/01/rdf-schema#label
|
SNP detection
|
|
http://edamontology.org/created_in
|
beta12orEarlier
|
|
http://www.geneontology.org/formats/oboInOwl#hasDefinition
|
Find single nucleotide polymorphisms (SNPs) - single nucleotide change in base positions - between sequences. Typically done for sequences from a high-throughput sequencing experiment that differ from a reference genome and which might, especially by reference to population frequency or functional data, indicate a polymorphism.
|
|
http://www.w3.org/1999/02/22-rdf-syntax-ns#type
|
http://www.w3.org/2002/07/owl#Class
|
|
http://www.geneontology.org/formats/oboInOwl#hasExactSynonym
|
SNP discovery |
| SNP calling |
| Single nucleotide polymorphism detection
|
|
http://www.w3.org/2000/01/rdf-schema#comment
|
This includes functional SNPs for large-scale genotyping purposes, disease-associated non-synonymous SNPs etc.
|
|
http://www.w3.org/2000/01/rdf-schema#subClassOf
|
http://edamontology.org/operation_3202
|
http://edamontology.org/operation_0480 |
|
http://www.geneontology.org/formats/oboInOwl#inSubset
|
http://purl.obolibrary.org/obo/edam#edam |
| http://purl.obolibrary.org/obo/edam#operations
|
|
http://www.w3.org/2000/01/rdf-schema#label
|
Side chain modelling
|
|
http://edamontology.org/created_in
|
beta12orEarlier
|
|
http://www.geneontology.org/formats/oboInOwl#hasNarrowSynonym
|
Rotamer likelihood prediction
|
|
http://www.geneontology.org/formats/oboInOwl#hasDefinition
|
Model, analyse or edit amino acid side chain conformation in protein structure, optimize side-chain packing, hydrogen bonding etc.
|
|
http://www.w3.org/1999/02/22-rdf-syntax-ns#type
|
http://www.w3.org/2002/07/owl#Class
|
|
http://www.geneontology.org/formats/oboInOwl#hasExactSynonym
|
Protein modelling (side chains)
|
|
http://www.w3.org/2000/01/rdf-schema#comment
|
Methods might use a residue rotamer library. |
| This includes rotamer likelihood prediction: the prediction of rotamer likelihoods for all 20 amino acid types at each position in a protein structure, where output typically includes, for each residue position, the likelihoods for the 20 amino acid types with estimated reliability of the 20 likelihoods.
|
|
http://www.w3.org/2000/01/rdf-schema#subClassOf
|
http://edamontology.org/operation_0477
|
http://edamontology.org/topic_0003 |
|
http://www.geneontology.org/formats/oboInOwl#inSubset
|
http://purl.obolibrary.org/obo/edam#topics |
| http://purl.obolibrary.org/obo/edam#edam
|
|
http://edamontology.org/notRecommendedForAnnotation
|
true
|
|
http://www.w3.org/2000/01/rdf-schema#label
|
Topic
|
|
http://edamontology.org/created_in
|
beta12orEarlier
|
|
http://www.w3.org/2000/01/rdf-schema#seeAlso
|
http://www.ifomis.org/bfo/1.1/snap#Continuant |
| http://onto.eva.mpg.de/ontologies/gfo-bio.owl#Method |
| http://www.loa-cnr.it/ontologies/DOLCE-Lite.owl#quality |
| http://purl.org/biotop/biotop.owl#Quality |
| http://www.onto-med.de/ontologies/gfo.owl#Category |
| http://bioontology.org/ontologies/ResearchArea.owl#Area_of_Research |
| http://www.onto-med.de/ontologies/gfo.owl#Perpetuant |
| http://www.ifomis.org/bfo/1.1/snap#Quality
|
|
http://www.geneontology.org/formats/oboInOwl#hasDefinition
|
A category denoting a rather broad domain or field of interest, of study, application, work, data, or technology. Topics have no clearly defined borders between each other.
|
|
http://www.w3.org/1999/02/22-rdf-syntax-ns#type
|
http://www.w3.org/2002/07/owl#Class
|
|
http://www.w3.org/2002/07/owl#disjointWith
|
http://www.w3.org/2002/07/owl#DeprecatedClass
|
|
http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym
|
sumo:FieldOfStudy
|
http://edamontology.org/operation_3223 |
|
http://www.geneontology.org/formats/oboInOwl#inSubset
|
http://purl.obolibrary.org/obo/edam#edam |
| http://purl.obolibrary.org/obo/edam#operations
|
|
http://www.w3.org/2000/01/rdf-schema#label
|
Differential gene expression analysis
|
|
http://edamontology.org/created_in
|
1.1
|
|
http://www.geneontology.org/formats/oboInOwl#hasDefinition
|
Identify from molecular sequence analysis (typically from analysis of microarray or RNA-seq data) genes whose expression levels are significantly different between two sample groups.
|
|
http://www.w3.org/1999/02/22-rdf-syntax-ns#type
|
http://www.w3.org/2002/07/owl#Class
|
|
http://www.geneontology.org/formats/oboInOwl#hasExactSynonym
|
Differentially expressed gene identification |
| Differential gene analysis
|
|
http://www.w3.org/2000/01/rdf-schema#comment
|
Differential gene expression analysis is used, for example, to identify which genes are up-regulated (increased expression) or down-regulated (decreased expression) between a group treated with a drug and a control groups.
|
|
http://www.w3.org/2000/01/rdf-schema#subClassOf
|
http://edamontology.org/operation_2998
|
http://edamontology.org/topic_1317 |
|
http://www.geneontology.org/formats/oboInOwl#inSubset
|
http://purl.obolibrary.org/obo/edam#events |
| http://purl.obolibrary.org/obo/edam#topics |
| http://purl.obolibrary.org/obo/edam#edam
|
|
http://edamontology.org/isdebtag
|
true
|
|
http://www.geneontology.org/formats/oboInOwl#hasDbXref
|
VT 1.5.24 Structural biology
|
|
http://www.w3.org/2000/01/rdf-schema#label
|
Structural biology
|
|
http://edamontology.org/created_in
|
beta12orEarlier
|
|
http://www.geneontology.org/formats/oboInOwl#hasNarrowSynonym
|
Structural assignment |
| Structure determination |
| Structural determination
|
|
http://www.w3.org/2000/01/rdf-schema#seeAlso
|
https://en.wikipedia.org/wiki/Structural_biology
|
|
http://www.geneontology.org/formats/oboInOwl#hasDefinition
|
The molecular structure of biological molecules, particularly macromolecules such as proteins and nucleic acids.
|
|
http://www.w3.org/1999/02/22-rdf-syntax-ns#type
|
http://www.w3.org/2002/07/owl#Class
|
|
http://www.w3.org/2000/01/rdf-schema#comment
|
This includes experimental methods for biomolecular structure determination, such as X-ray crystallography, nuclear magnetic resonance (NMR), circular dichroism (CD) spectroscopy, microscopy etc., including the assignment or modelling of molecular structure from such data.
|
|
http://www.geneontology.org/formats/oboInOwl#hasHumanReadableId
|
Structural_biology
|
|
http://www.w3.org/2000/01/rdf-schema#subClassOf
|
http://edamontology.org/topic_3070
|
http://edamontology.org/data_2048 |
|
http://www.geneontology.org/formats/oboInOwl#inSubset
|
http://purl.obolibrary.org/obo/edam#edam |
| http://purl.obolibrary.org/obo/edam#data
|
|
http://www.w3.org/2000/01/rdf-schema#label
|
Report
|
|
http://edamontology.org/created_in
|
beta12orEarlier
|
|
http://www.w3.org/2000/01/rdf-schema#seeAlso
|
http://semanticscience.org/resource/SIO_000148
|
|
http://www.geneontology.org/formats/oboInOwl#hasDefinition
|
A human-readable collection of information including annotation on a biological entity or phenomena, computer-generated reports of analysis of primary data (e.g. sequence or structural), and metadata (data about primary data) or any other free (essentially unformatted) text, as distinct from the primary data itself.
|
|
http://www.w3.org/1999/02/22-rdf-syntax-ns#type
|
http://www.w3.org/2002/07/owl#Class
|
|
http://www.geneontology.org/formats/oboInOwl#hasExactSynonym
|
Record |
| Document
|
|
http://www.w3.org/2000/01/rdf-schema#comment
|
You can use this term by default for any textual report, in case you can't find another, more specific term. Reports may be generated automatically or collated by hand and can include metadata on the origin, source, history, ownership or location of some thing.
|
|
http://www.w3.org/2000/01/rdf-schema#subClassOf
|
http://edamontology.org/data_0006
|
http://edamontology.org/data_2044 |
|
http://www.geneontology.org/formats/oboInOwl#inSubset
|
http://purl.obolibrary.org/obo/edam#edam |
| http://purl.obolibrary.org/obo/edam#data
|
|
http://www.w3.org/2000/01/rdf-schema#label
|
Sequence
|
|
http://edamontology.org/created_in
|
beta12orEarlier
|
|
http://www.w3.org/2000/01/rdf-schema#seeAlso
|
http://purl.bioontology.org/ontology/MSH/D008969 |
| http://purl.org/biotop/biotop.owl#BioMolecularSequenceInformation
|
|
http://www.geneontology.org/formats/oboInOwl#hasDefinition
|
One or more molecular sequences, possibly with associated annotation.
|
|
http://www.w3.org/1999/02/22-rdf-syntax-ns#type
|
http://www.w3.org/2002/07/owl#Class
|
|
http://www.geneontology.org/formats/oboInOwl#hasExactSynonym
|
Sequences
|
|
http://www.w3.org/2000/01/rdf-schema#comment
|
This concept is a placeholder of concepts for primary sequence data including raw sequences and sequence records. It should not normally be used for derivatives such as sequence alignments, motifs or profiles.
|
|
http://www.w3.org/2000/01/rdf-schema#subClassOf
|
_:579 |
| http://edamontology.org/data_0006
|
http://edamontology.org/has_input |
|
http://purl.obolibrary.org/obo/is_anti_symmetric
|
false
|
|
http://www.w3.org/2000/01/rdf-schema#label
|
has input
|
|
http://purl.obolibrary.org/obo/is_reflexive
|
false
|
|
http://www.geneontology.org/formats/oboInOwl#isCyclic
|
true
|
|
http://www.w3.org/2000/01/rdf-schema#range
|
http://edamontology.org/data_0006
|
|
http://www.geneontology.org/formats/oboInOwl#inSubset
|
edam |
| relations
|
|
http://purl.obolibrary.org/obo/is_symmetric
|
false
|
|
http://www.w3.org/2000/01/rdf-schema#domain
|
http://edamontology.org/operation_0004
|
|
http://www.w3.org/2002/07/owl#inverseOf
|
http://edamontology.org/is_input_of
|
|
http://www.w3.org/2000/01/rdf-schema#seeAlso
|
"http://purl.obolibrary.org/obo/OBI_0000293" |
| http://wsio.org/has_input
|
|
http://www.geneontology.org/formats/oboInOwl#hasDefinition
|
'A has_input B' defines for the subject A, that it has the object B as a necessary or actual input or input argument.
|
|
http://www.w3.org/1999/02/22-rdf-syntax-ns#type
|
http://www.w3.org/2002/07/owl#ObjectProperty
|
|
http://www.w3.org/2000/01/rdf-schema#comment
|
Subject A can either be concept that is or has an 'Operation' function, or an entity outside of an ontology (or an ontology concept in a role of an entity being semantically annotated) that has an 'Operation' function or is an 'Operation'. Object B can be any concept or entity. In EDAM, only 'has_input' is explicitly defined between EDAM concepts ('Operation' 'has_input' 'Data'). The inverse, 'is_input_of', is not explicitly defined.
|
|
http://purl.obolibrary.org/obo/transitive_over
|
OBO_REL:is_a
|
|
http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym
|
OBO_REL:has_participant
|
http://edamontology.org/topic_0081 |
|
http://www.geneontology.org/formats/oboInOwl#inSubset
|
http://purl.obolibrary.org/obo/edam#events |
| http://purl.obolibrary.org/obo/edam#topics |
| http://purl.obolibrary.org/obo/edam#edam
|
|
http://edamontology.org/isdebtag
|
true
|
|
http://www.w3.org/2000/01/rdf-schema#label
|
Structure analysis
|
|
http://edamontology.org/created_in
|
beta12orEarlier
|
|
http://www.geneontology.org/formats/oboInOwl#hasNarrowSynonym
|
Structure data resources |
| Structures |
| Molecular structure |
| Structure databases |
| Computational structural biology
|
|
http://www.w3.org/2000/01/rdf-schema#seeAlso
|
http://purl.bioontology.org/ontology/MSH/D015394
|
|
http://www.geneontology.org/formats/oboInOwl#hasDefinition
|
The curation, processing and analysis of the structure of biological molecules, typically proteins and nucleic acids and other macromolecules.
|
|
http://www.w3.org/1999/02/22-rdf-syntax-ns#type
|
http://www.w3.org/2002/07/owl#Class
|
|
http://www.geneontology.org/formats/oboInOwl#hasExactSynonym
|
Biomolecular structure |
| Structural bioinformatics
|
|
http://www.w3.org/2000/01/rdf-schema#comment
|
This includes related concepts such as structural properties, alignments and structural motifs.
|
|
http://www.geneontology.org/formats/oboInOwl#hasHumanReadableId
|
Structure_analysis
|
|
http://www.w3.org/2000/01/rdf-schema#subClassOf
|
http://edamontology.org/topic_3307
|
http://edamontology.org/topic_0084 |
|
http://www.geneontology.org/formats/oboInOwl#inSubset
|
http://purl.obolibrary.org/obo/edam#events |
| http://purl.obolibrary.org/obo/edam#topics |
| http://purl.obolibrary.org/obo/edam#edam
|
|
http://edamontology.org/isdebtag
|
true
|
|
http://www.w3.org/2000/01/rdf-schema#label
|
Phylogeny
|
|
http://edamontology.org/created_in
|
beta12orEarlier
|
|
http://www.geneontology.org/formats/oboInOwl#hasNarrowSynonym
|
Phylogenetic clocks |
| Phylogenetic stratigraphy |
| Phylogenetic dating |
| Phylogeny reconstruction |
| Phylogenetic simulation
|
|
http://www.w3.org/2000/01/rdf-schema#seeAlso
|
https://en.wikipedia.org/wiki/Phylogenetic_tree |
| http://purl.bioontology.org/ontology/MSH/D010802
|
|
http://www.geneontology.org/formats/oboInOwl#hasDefinition
|
The study of evolutionary relationships amongst organisms.
|
|
http://www.w3.org/1999/02/22-rdf-syntax-ns#type
|
http://www.w3.org/2002/07/owl#Class
|
|
http://www.w3.org/2000/01/rdf-schema#comment
|
This includes diverse phylogenetic methods, including phylogenetic tree construction, typically from molecular sequence or morphological data, methods that simulate DNA sequence evolution, a phylogenetic tree or the underlying data, or which estimate or use molecular clock and stratigraphic (age) data, methods for studying gene evolution etc.
|
|
http://www.w3.org/2000/01/rdf-schema#subClassOf
|
http://edamontology.org/topic_3307 |
| http://edamontology.org/topic_3299
|
|
http://www.geneontology.org/formats/oboInOwl#hasHumanReadableId
|
Phylogeny
|
http://edamontology.org/topic_0082 |
|
http://www.geneontology.org/formats/oboInOwl#inSubset
|
http://purl.obolibrary.org/obo/edam#topics |
| http://purl.obolibrary.org/obo/edam#edam
|
|
http://edamontology.org/isdebtag
|
true
|
|
http://www.w3.org/2000/01/rdf-schema#label
|
Structure prediction
|
|
http://edamontology.org/created_in
|
beta12orEarlier
|
|
http://www.geneontology.org/formats/oboInOwl#hasNarrowSynonym
|
Nucleic acid design |
| DNA structure prediction |
| Nucleic acid folding |
| Protein structure prediction |
| RNA structure prediction |
| Protein fold recognition |
| Nucleic acid structure prediction
|
|
http://www.w3.org/2000/01/rdf-schema#seeAlso
|
https://en.wikipedia.org/wiki/Nucleic_acid_structure_prediction |
| https://en.wikipedia.org/wiki/Protein_structure_prediction
|
|
http://www.geneontology.org/formats/oboInOwl#hasDefinition
|
The prediction of molecular structure, including the prediction, modelling, recognition or design of protein secondary or tertiary structure or other structural features, and the folding of nucleic acid molecules and the prediction or design of nucleic acid (typically RNA) sequences with specific conformations.
|
|
http://www.w3.org/1999/02/22-rdf-syntax-ns#type
|
http://www.w3.org/2002/07/owl#Class
|
|
http://www.w3.org/2000/01/rdf-schema#comment
|
This includes the recognition (prediction and assignment) of known protein structural domains or folds in protein sequence(s), for example by threading, or the alignment of molecular sequences to structures, structural (3D) profiles or templates (representing a structure or structure alignment).
|
|
http://www.w3.org/2000/01/rdf-schema#subClassOf
|
http://edamontology.org/topic_0081
|
|
http://www.geneontology.org/formats/oboInOwl#hasHumanReadableId
|
Structure_prediction
|
http://edamontology.org/data_1583 |
|
http://www.geneontology.org/formats/oboInOwl#inSubset
|
http://purl.obolibrary.org/obo/edam#edam |
| http://purl.obolibrary.org/obo/edam#data
|
|
http://www.geneontology.org/formats/oboInOwl#comment
|
Nucleic acid melting curve: a melting curve of a double-stranded nucleic acid molecule (DNA or DNA/RNA). Shows the proportion of nucleic acid which are double-stranded versus temperature. |
| Nucleic acid stitch profile: stitch profile of hybridised or double stranded nucleic acid (DNA or RNA/DNA). A stitch profile diagram shows partly melted DNA conformations (with probabilities) at a range of temperatures. For example, a stitch profile might show possible loop openings with their location, size, probability and fluctuations at a given temperature. |
| Nucleic acid probability profile: a probability profile of a double-stranded nucleic acid molecule (DNA or DNA/RNA). Shows the probability of a base pair not being melted (i.e. remaining as double-stranded DNA) at a specified temperature |
| Nucleic acid temperature profile: a temperature profile of a double-stranded nucleic acid molecule (DNA or DNA/RNA). Plots melting temperature versus base position.
|
|
http://www.w3.org/2000/01/rdf-schema#label
|
Nucleic acid melting profile
|
|
http://edamontology.org/created_in
|
beta12orEarlier
|
|
http://www.geneontology.org/formats/oboInOwl#hasNarrowSynonym
|
Melting map |
| Nucleic acid melting curve
|
|
http://www.geneontology.org/formats/oboInOwl#hasDefinition
|
Data on the dissociation characteristics of a double-stranded nucleic acid molecule (DNA or a DNA/RNA hybrid) during heating.
|
|
http://www.w3.org/1999/02/22-rdf-syntax-ns#type
|
http://www.w3.org/2002/07/owl#Class
|
|
http://www.geneontology.org/formats/oboInOwl#hasExactSynonym
|
Nucleic acid stability profile
|
|
http://www.w3.org/2000/01/rdf-schema#comment
|
A melting (stability) profile calculated the free energy required to unwind and separate the nucleic acid strands, plotted for sliding windows over a sequence.
|
|
http://www.w3.org/2000/01/rdf-schema#subClassOf
|
http://edamontology.org/data_2985
|
http://edamontology.org/topic_0089 |
|
http://www.geneontology.org/formats/oboInOwl#inSubset
|
http://purl.obolibrary.org/obo/edam#events |
| http://purl.obolibrary.org/obo/edam#topics |
| http://purl.obolibrary.org/obo/edam#edam
|
|
http://edamontology.org/isdebtag
|
true
|
|
http://www.w3.org/2000/01/rdf-schema#label
|
Ontology and terminology
|
|
http://edamontology.org/created_in
|
beta12orEarlier
|
|
http://www.geneontology.org/formats/oboInOwl#hasNarrowSynonym
|
Upper ontology |
| Applied ontology |
| Ontology |
| Ontology relations |
| Ontologies |
| Terminology
|
|
http://www.w3.org/2000/01/rdf-schema#seeAlso
|
http://purl.bioontology.org/ontology/MSH/D002965 |
| https://en.wikipedia.org/wiki/Ontology_(information_science)
|
|
http://www.geneontology.org/formats/oboInOwl#hasDefinition
|
The conceptualisation, categorisation and nomenclature (naming) of entities or phenomena within biology or bioinformatics. This includes formal ontologies, controlled vocabularies, structured glossary, symbols and terminology or other related resource.
|
|
http://www.w3.org/1999/02/22-rdf-syntax-ns#type
|
http://www.w3.org/2002/07/owl#Class
|
|
http://www.w3.org/2000/01/rdf-schema#subClassOf
|
http://edamontology.org/topic_0605
|
|
http://www.geneontology.org/formats/oboInOwl#hasHumanReadableId
|
Ontology_and_terminology
|
http://edamontology.org/format_2350 |
|
http://www.geneontology.org/formats/oboInOwl#inSubset
|
http://purl.obolibrary.org/obo/edam#formats |
| http://purl.obolibrary.org/obo/edam#edam
|
|
http://edamontology.org/notRecommendedForAnnotation
|
true
|
|
http://www.w3.org/2000/01/rdf-schema#label
|
Format (by type of data)
|
|
http://edamontology.org/created_in
|
beta12orEarlier
|
|
http://www.geneontology.org/formats/oboInOwl#hasDefinition
|
A placeholder concept for visual navigation by dividing data formats by the content of the data that is represented.
|
|
http://www.w3.org/1999/02/22-rdf-syntax-ns#type
|
http://www.w3.org/2002/07/owl#Class
|
|
http://www.geneontology.org/formats/oboInOwl#hasExactSynonym
|
Format (typed)
|
|
http://www.w3.org/2000/01/rdf-schema#comment
|
This concept exists only to assist EDAM maintenance and navigation in graphical browsers. It does not add semantic information. The concept branch under 'Format (typed)' provides an alternative organisation of the concepts nested under the other top-level branches ('Binary', 'HTML', 'RDF', 'Text' and 'XML'. All concepts under here are already included under those branches.
|
|
http://www.w3.org/2000/01/rdf-schema#subClassOf
|
http://edamontology.org/format_1915
|
http://edamontology.org/data_1596 |
|
http://www.geneontology.org/formats/oboInOwl#inSubset
|
http://purl.obolibrary.org/obo/edam#edam |
| http://purl.obolibrary.org/obo/edam#data
|
|
http://www.w3.org/2000/01/rdf-schema#label
|
Nucleic acid folding report
|
|
http://edamontology.org/created_in
|
beta12orEarlier
|
|
http://www.geneontology.org/formats/oboInOwl#hasNarrowSynonym
|
RNA secondary structure folding classification |
| RNA secondary structure folding probablities
|
|
http://www.geneontology.org/formats/oboInOwl#hasDefinition
|
A human-readable collection of information about RNA/DNA folding, minimum folding energies for DNA or RNA sequences, energy landscape of RNA mutants etc.
|
|
http://www.w3.org/1999/02/22-rdf-syntax-ns#type
|
http://www.w3.org/2002/07/owl#Class
|
|
http://www.geneontology.org/formats/oboInOwl#hasExactSynonym
|
Nucleic acid report (folding) |
| Nucleic acid report (folding model)
|
|
http://www.w3.org/2000/01/rdf-schema#subClassOf
|
http://edamontology.org/data_2084
|
http://edamontology.org/format_2330 |
|
http://www.geneontology.org/formats/oboInOwl#inSubset
|
http://purl.obolibrary.org/obo/edam#formats |
| http://purl.obolibrary.org/obo/edam#edam
|
|
http://www.w3.org/2000/01/rdf-schema#label
|
Textual format
|
|
http://edamontology.org/created_in
|
beta12orEarlier
|
|
http://www.geneontology.org/formats/oboInOwl#hasNarrowSynonym
|
Plain text format |
| txt
|
|
http://www.w3.org/2000/01/rdf-schema#seeAlso
|
http://www.iana.org/assignments/media-types/text/plain |
| http://filext.com/file-extension/TXT |
| http://www.iana.org/assignments/media-types/media-types.xhtml#text
|
|
http://www.geneontology.org/formats/oboInOwl#hasDefinition
|
Textual format.
|
|
http://www.w3.org/1999/02/22-rdf-syntax-ns#type
|
http://www.w3.org/2002/07/owl#Class
|
|
http://www.w3.org/2002/07/owl#disjointWith
|
http://edamontology.org/format_2333
|
|
http://www.w3.org/2000/01/rdf-schema#comment
|
Data in text format can be compressed into binary format, or can be a value of an XML element or attribute. Markup formats are not considered textual (or more precisely, not plain-textual).
|
|
http://www.w3.org/2000/01/rdf-schema#subClassOf
|
http://edamontology.org/format_1915
|
http://edamontology.org/data_2012 |
|
http://www.geneontology.org/formats/oboInOwl#inSubset
|
http://purl.obolibrary.org/obo/edam#edam |
| http://purl.obolibrary.org/obo/edam#data
|
|
http://www.geneontology.org/formats/oboInOwl#hasDbXref
|
Moby:MapPosition |
| PDBML:_atom_site.id |
| Moby:Position |
| Moby:Locus |
| Moby:GCP_MapInterval |
| Moby:GCP_MapPoint |
| Moby:GCP_MapPosition |
| Moby:GenePosition |
| Moby:HitPosition
|
|
http://www.w3.org/2000/01/rdf-schema#label
|
Sequence coordinates
|
|
http://edamontology.org/created_in
|
beta12orEarlier
|
|
http://www.geneontology.org/formats/oboInOwl#hasDefinition
|
A position in a map (for example a genetic map), either a single position (point) or a region / interval.
|
|
http://www.w3.org/1999/02/22-rdf-syntax-ns#type
|
http://www.w3.org/2002/07/owl#Class
|
|
http://www.geneontology.org/formats/oboInOwl#hasExactSynonym
|
Locus |
| Sequence co-ordinates |
| Map position
|
|
http://www.w3.org/2000/01/rdf-schema#comment
|
This includes positions in genomes based on a reference sequence. A position may be specified for any mappable object, i.e. anything that may have positional information such as a physical position in a chromosome. Data might include sequence region name, strand, coordinate system name, assembly name, start position and end position.
|
|
http://www.w3.org/2000/01/rdf-schema#subClassOf
|
http://edamontology.org/data_1016 |
| http://edamontology.org/data_0006 |
| http://edamontology.org/data_1017
|
http://edamontology.org/topic_3168 |
|
http://www.geneontology.org/formats/oboInOwl#inSubset
|
http://purl.obolibrary.org/obo/edam#events |
| http://purl.obolibrary.org/obo/edam#topics |
| http://purl.obolibrary.org/obo/edam#edam
|
|
http://edamontology.org/isdebtag
|
true
|
|
http://www.w3.org/2000/01/rdf-schema#label
|
Sequencing
|
|
http://edamontology.org/created_in
|
1.1
|
|
http://www.geneontology.org/formats/oboInOwl#hasNarrowSynonym
|
Amplicon sequencing |
| High throughput sequencing |
| Chromosome walking |
| DNase-Seq |
| Next gen sequencing |
| Clone verification |
| Resequencing |
| Primer walking |
| Next generation sequencing |
| NGS |
| Sanger sequencing |
| High-throughput sequencing |
| Small RNA sequencing
|
|
http://www.w3.org/2000/01/rdf-schema#seeAlso
|
http://purl.bioontology.org/ontology/MSH/D059014 |
| https://en.wikipedia.org/wiki/Sequencing
|
|
http://www.geneontology.org/formats/oboInOwl#hasDefinition
|
The determination of complete (typically nucleotide) sequences, including those of genomes (full genome sequencing, de novo sequencing and resequencing), amplicons and transcriptomes.
|
|
http://www.w3.org/1999/02/22-rdf-syntax-ns#type
|
http://www.w3.org/2002/07/owl#Class
|
|
http://www.geneontology.org/formats/oboInOwl#hasExactSynonym
|
DNA-Seq
|
|
http://www.w3.org/2000/01/rdf-schema#comment
|
Amplicon sequencing is the ultra-deep sequencing of PCR products (amplicons), usually for the purpose of efficient genetic variant identification and characterisation in specific genomic regions.
|
|
http://www.w3.org/2000/01/rdf-schema#subClassOf
|
http://edamontology.org/topic_3361
|
|
http://www.geneontology.org/formats/oboInOwl#hasHumanReadableId
|
Sequencing
|
http://edamontology.org/data_1539 |
|
http://www.geneontology.org/formats/oboInOwl#inSubset
|
http://purl.obolibrary.org/obo/edam#edam |
| http://purl.obolibrary.org/obo/edam#data
|
|
http://www.w3.org/2000/01/rdf-schema#label
|
Protein structural quality report
|
|
http://edamontology.org/created_in
|
beta12orEarlier
|
|
http://www.geneontology.org/formats/oboInOwl#hasDefinition
|
Report on the quality of a protein three-dimensional model.
|
|
http://www.w3.org/1999/02/22-rdf-syntax-ns#type
|
http://www.w3.org/2002/07/owl#Class
|
|
http://www.geneontology.org/formats/oboInOwl#hasExactSynonym
|
Protein report (structural quality) |
| Protein structure report (quality evaluation) |
| Protein property (structural quality) |
| Protein structure validation report
|
|
http://www.w3.org/2000/01/rdf-schema#comment
|
Model validation might involve checks for atomic packing, steric clashes, agreement with electron density maps etc.
|
|
http://www.w3.org/2000/01/rdf-schema#subClassOf
|
http://edamontology.org/data_1537
|
http://edamontology.org/data_1534 |
|
http://www.geneontology.org/formats/oboInOwl#inSubset
|
http://purl.obolibrary.org/obo/edam#edam |
| http://purl.obolibrary.org/obo/edam#data
|
|
http://www.w3.org/2000/01/rdf-schema#label
|
Peptide immunogenicity data
|
|
http://edamontology.org/created_in
|
beta12orEarlier
|
|
http://www.geneontology.org/formats/oboInOwl#hasDefinition
|
An report on allergenicity / immunogenicity of peptides and proteins.
|
|
http://www.w3.org/1999/02/22-rdf-syntax-ns#type
|
http://www.w3.org/2002/07/owl#Class
|
|
http://www.geneontology.org/formats/oboInOwl#hasExactSynonym
|
Peptide immunogenicity |
| Peptide immunogenicity report
|
|
http://www.w3.org/2000/01/rdf-schema#comment
|
This includes data on peptide ligands that elicit an immune response (immunogens), allergic cross-reactivity, predicted antigenicity (Hopp and Woods plot) etc. These data are useful in the development of peptide-specific antibodies or multi-epitope vaccines. Methods might use sequence data (for example motifs) and / or structural data.
|
|
http://www.w3.org/2000/01/rdf-schema#subClassOf
|
http://edamontology.org/data_0897
|
http://edamontology.org/topic_0097 |
|
http://www.geneontology.org/formats/oboInOwl#inSubset
|
http://purl.obolibrary.org/obo/edam#topics |
| http://purl.obolibrary.org/obo/edam#edam
|
|
http://www.w3.org/2000/01/rdf-schema#label
|
Nucleic acid structure analysis
|
|
http://edamontology.org/created_in
|
beta12orEarlier
|
|
http://www.geneontology.org/formats/oboInOwl#hasNarrowSynonym
|
Nucleic acid thermodynamics |
| RNA alignment |
| RNA structure |
| DNA melting |
| RNA structure alignment |
| Nucleic acid denaturation |
| DNA structure
|
|
http://www.w3.org/2000/01/rdf-schema#seeAlso
|
https://en.wikipedia.org/wiki/Nucleic_acid_structure
|
|
http://www.geneontology.org/formats/oboInOwl#hasDefinition
|
The archival, curation, processing and analysis of nucleic acid structural information, such as whole structures, structural features and alignments, and associated annotation.
|
|
http://www.w3.org/1999/02/22-rdf-syntax-ns#type
|
http://www.w3.org/2002/07/owl#Class
|
|
http://www.geneontology.org/formats/oboInOwl#hasExactSynonym
|
Nucleic acid structure
|
|
http://www.w3.org/2000/01/rdf-schema#comment
|
Includes secondary and tertiary nucleic acid structural data, nucleic acid thermodynamic, thermal and conformational properties including DNA or DNA/RNA denaturation (melting) etc.
|
|
http://www.w3.org/2000/01/rdf-schema#subClassOf
|
http://edamontology.org/topic_0081 |
| http://edamontology.org/topic_0077
|
|
http://www.geneontology.org/formats/oboInOwl#hasHumanReadableId
|
Nucleic_acid_structure_analysis
|
http://edamontology.org/topic_3125 |
|
http://www.geneontology.org/formats/oboInOwl#inSubset
|
http://purl.obolibrary.org/obo/edam#topics |
| http://purl.obolibrary.org/obo/edam#edam
|
|
http://www.w3.org/2000/01/rdf-schema#label
|
DNA binding sites
|
|
http://www.geneontology.org/formats/oboInOwl#hasAlternativeId
|
http://edamontology.org/data_3125
|
|
http://edamontology.org/created_in
|
beta13
|
|
http://www.geneontology.org/formats/oboInOwl#hasNarrowSynonym
|
Restriction sites |
| Matrix-attachment region |
| Nucleosome exclusion sequences |
| Matrix/scaffold attachment region |
| Scaffold-attachment region |
| Ribosome binding sites
|
|
http://www.w3.org/2000/01/rdf-schema#seeAlso
|
https://en.wikipedia.org/wiki/DNA_binding_site
|
|
http://www.geneontology.org/formats/oboInOwl#hasDefinition
|
Nucleic acids binding to some other molecule.
|
|
http://www.w3.org/1999/02/22-rdf-syntax-ns#type
|
http://www.w3.org/2002/07/owl#Class
|
|
http://www.w3.org/2000/01/rdf-schema#comment
|
This includes sites involved with DNA replication and recombination. This includes binding sites for initiation of replication (origin of replication), regions where transfer is initiated during the conjugation or mobilisation (origin of transfer), starting sites for DNA duplication (origin of replication) and regions which are eliminated through any of kind of recombination. Also nucleosome exclusion regions, i.e. specific patterns or regions which exclude nucleosomes (the basic structural units of eukaryotic chromatin which play a significant role in regulating gene expression). |
| This includes ribosome binding sites (Shine-Dalgarno sequence in prokaryotes), restriction enzyme recognition sites (restriction sites) etc.
|
|
http://www.geneontology.org/formats/oboInOwl#hasHumanReadableId
|
DNA_binding_sites
|
|
http://www.w3.org/2000/01/rdf-schema#subClassOf
|
http://edamontology.org/topic_3511 |
| http://edamontology.org/topic_0654
|
http://edamontology.org/operation_3211 |
|
http://www.geneontology.org/formats/oboInOwl#inSubset
|
http://purl.obolibrary.org/obo/edam#edam |
| http://purl.obolibrary.org/obo/edam#operations
|
|
http://www.w3.org/2000/01/rdf-schema#label
|
Genome indexing
|
|
http://edamontology.org/created_in
|
1.1
|
|
http://www.geneontology.org/formats/oboInOwl#hasNarrowSynonym
|
Suffix arrays |
| Genome indexing (Burrows-Wheeler) |
| Burrows-Wheeler |
| Genome indexing (suffix arrays)
|
|
http://www.geneontology.org/formats/oboInOwl#hasDefinition
|
Generate an index of a genome sequence.
|
|
http://www.w3.org/1999/02/22-rdf-syntax-ns#type
|
http://www.w3.org/2002/07/owl#Class
|
|
http://www.w3.org/2000/01/rdf-schema#comment
|
Many sequence alignment tasks involving many or very large sequences rely on a precomputed index of the sequence to accelerate the alignment. The Burrows-Wheeler Transform (BWT) is a permutation of the genome based on a suffix array algorithm. A suffix array consists of the lexicographically sorted list of suffixes of a genome.
|
|
http://www.w3.org/2000/01/rdf-schema#subClassOf
|
_:515 |
| http://edamontology.org/operation_0227
|
http://edamontology.org/format_1915 |
|
http://www.geneontology.org/formats/oboInOwl#inSubset
|
http://purl.obolibrary.org/obo/edam#formats |
| http://purl.obolibrary.org/obo/edam#edam
|
|
http://edamontology.org/notRecommendedForAnnotation
|
true
|
|
http://www.w3.org/2000/01/rdf-schema#label
|
Format
|
|
http://edamontology.org/created_in
|
beta12orEarlier
|
|
http://www.geneontology.org/formats/oboInOwl#hasNarrowSynonym
|
File format
|
|
http://www.w3.org/2000/01/rdf-schema#seeAlso
|
http://www.onto-med.de/ontologies/gfo.owl#Symbol_structure |
| http://en.wikipedia.org/wiki/List_of_file_formats |
| http://semanticscience.org/resource/SIO_000618 |
| http://www.ifomis.org/bfo/1.1/snap#Quality |
| http://semanticscience.org/resource/SIO_000612 |
| http://www.ifomis.org/bfo/1.1/snap#Continuant |
| http://en.wikipedia.org/wiki/File_format |
| "http://purl.obolibrary.org/obo/IAO_0000098" |
| http://www.loa-cnr.it/ontologies/DOLCE-Lite.owl#quality |
| http://purl.org/biotop/biotop.owl#Quality |
| "http://purl.org/dc/elements/1.1/format" |
| http://wsio.org/compression_004 |
| http://www.onto-med.de/ontologies/gfo.owl#Perpetuant |
| http://purl.org/biotop/biotop.owl#MachineLanguage
|
|
http://www.geneontology.org/formats/oboInOwl#hasDefinition
|
A defined way or layout of representing and structuring data in a computer file, blob, string, message, or elsewhere.
|
|
http://www.w3.org/1999/02/22-rdf-syntax-ns#type
|
http://www.w3.org/2002/07/owl#Class
|
|
http://www.w3.org/2002/07/owl#disjointWith
|
http://www.w3.org/2002/07/owl#DeprecatedClass |
| http://edamontology.org/operation_0004 |
| http://edamontology.org/topic_0003
|
|
http://www.geneontology.org/formats/oboInOwl#hasExactSynonym
|
Data format |
| Exchange format
|
|
http://www.w3.org/2000/01/rdf-schema#comment
|
The main focus in EDAM lies on formats as means of structuring data exchanged between different tools or resources. The serialisation, compression, or encoding of concrete data formats/models is not in scope of EDAM. Format 'is format of' Data.
|
|
http://www.geneontology.org/formats/oboInOwl#hasBroadSynonym
|
Data model
|
http://edamontology.org/topic_0114 |
|
http://www.geneontology.org/formats/oboInOwl#inSubset
|
http://purl.obolibrary.org/obo/edam#topics |
| http://purl.obolibrary.org/obo/edam#edam
|
|
http://edamontology.org/isdebtag
|
true
|
|
http://www.w3.org/2000/01/rdf-schema#label
|
Gene structure
|
|
http://edamontology.org/created_in
|
beta12orEarlier
|
|
http://www.geneontology.org/formats/oboInOwl#hasNarrowSynonym
|
Fusion genes
|
|
http://www.w3.org/2000/01/rdf-schema#seeAlso
|
https://en.wikipedia.org/wiki/Gene_structure
|
|
http://www.geneontology.org/formats/oboInOwl#hasDefinition
|
Gene structure, regions which make an RNA product and features such as promoters, coding regions, gene fusion, splice sites etc.
|
|
http://www.w3.org/1999/02/22-rdf-syntax-ns#type
|
http://www.w3.org/2002/07/owl#Class
|
|
http://www.geneontology.org/formats/oboInOwl#hasExactSynonym
|
Gene features
|
|
http://www.w3.org/2000/01/rdf-schema#comment
|
This includes the study of promoters, coding regions etc. |
| This incudes operons (operators, promoters and genes) from a bacterial genome. For example the operon leader and trailer gene, gene composition of the operon and associated information.
|
|
http://www.w3.org/2000/01/rdf-schema#subClassOf
|
http://edamontology.org/topic_3321
|
|
http://www.geneontology.org/formats/oboInOwl#hasHumanReadableId
|
Gene_structure
|
http://edamontology.org/topic_0128 |
|
http://www.geneontology.org/formats/oboInOwl#inSubset
|
http://purl.obolibrary.org/obo/edam#topics |
| http://purl.obolibrary.org/obo/edam#edam
|
|
http://edamontology.org/isdebtag
|
true
|
|
http://www.w3.org/2000/01/rdf-schema#label
|
Protein interactions
|
|
http://edamontology.org/created_in
|
beta12orEarlier
|
|
http://www.geneontology.org/formats/oboInOwl#hasNarrowSynonym
|
Protein-protein interactions |
| Protein-ligand interactions |
| Protein interaction map |
| Protein-RNA interactions |
| Protein-RNA interaction |
| Protein interactome |
| Protein-nucleic acid interactions |
| Protein interaction networks |
| Protein-DNA interactions |
| Protein-DNA interaction
|
|
http://www.w3.org/2000/01/rdf-schema#seeAlso
|
https://en.wikipedia.org/wiki/Protein%E2%80%93protein_interaction
|
|
http://www.geneontology.org/formats/oboInOwl#hasDefinition
|
Protein-protein, protein-DNA/RNA and protein-ligand interactions, including analysis of known interactions and prediction of putative interactions.
|
|
http://www.w3.org/1999/02/22-rdf-syntax-ns#type
|
http://www.w3.org/2002/07/owl#Class
|
|
http://www.w3.org/2000/01/rdf-schema#comment
|
This includes experimental (e.g. yeast two-hybrid) and computational analysis techniques.
|
|
http://www.w3.org/2000/01/rdf-schema#subClassOf
|
http://edamontology.org/topic_0602 |
| http://edamontology.org/topic_0078
|
|
http://www.geneontology.org/formats/oboInOwl#hasHumanReadableId
|
Protein_interactions
|
http://edamontology.org/topic_0121 |
|
http://www.geneontology.org/formats/oboInOwl#inSubset
|
http://purl.obolibrary.org/obo/edam#events |
| http://purl.obolibrary.org/obo/edam#topics |
| http://purl.obolibrary.org/obo/edam#edam
|
|
http://edamontology.org/isdebtag
|
true
|
|
http://www.w3.org/2000/01/rdf-schema#label
|
Proteomics
|
|
http://edamontology.org/created_in
|
beta12orEarlier
|
|
http://www.geneontology.org/formats/oboInOwl#hasNarrowSynonym
|
Bottom-up proteomics |
| Peptide identification |
| Targeted proteomics |
| Discovery proteomics |
| Protein and peptide identification |
| Top-down proteomics |
| Metaproteomics
|
|
http://www.w3.org/2000/01/rdf-schema#seeAlso
|
https://en.wikipedia.org/wiki/Proteomics |
| http://purl.bioontology.org/ontology/MSH/D040901
|
|
http://www.geneontology.org/formats/oboInOwl#hasDefinition
|
Protein and peptide identification, especially in the study of whole proteomes of organisms.
|
|
http://www.w3.org/1999/02/22-rdf-syntax-ns#type
|
http://www.w3.org/2002/07/owl#Class
|
|
http://www.w3.org/2000/01/rdf-schema#comment
|
Includes metaproteomics: proteomics analysis of an environmental sample. |
| Proteomics includes any methods (especially high-throughput) that separate, characterize and identify expressed proteins such as mass spectrometry, two-dimensional gel electrophoresis and protein microarrays, as well as in-silico methods that perform proteolytic or mass calculations on a protein sequence and other analyses of protein production data, for example in different cells or tissues.
|
|
http://www.w3.org/2000/01/rdf-schema#subClassOf
|
http://edamontology.org/topic_3391
|
|
http://www.geneontology.org/formats/oboInOwl#hasHumanReadableId
|
Proteomics
|
http://edamontology.org/topic_0102 |
|
http://www.geneontology.org/formats/oboInOwl#inSubset
|
http://purl.obolibrary.org/obo/edam#topics
|
|
http://edamontology.org/isdebtag
|
true
|
|
http://www.w3.org/2000/01/rdf-schema#label
|
Mapping
|
|
http://edamontology.org/created_in
|
beta12orEarlier
|
|
http://www.geneontology.org/formats/oboInOwl#hasNarrowSynonym
|
Synteny |
| Linkage |
| Linkage mapping |
| Genetic linkage
|
|
http://www.w3.org/2000/01/rdf-schema#seeAlso
|
https://en.wikipedia.org/wiki/Gene_mapping
|
|
http://www.geneontology.org/formats/oboInOwl#hasDefinition
|
The mapping of complete (typically nucleotide) sequences. Mapping (in the sense of short read alignment, or more generally, just alignment) has application in RNA-Seq analysis (mapping of transcriptomics reads), variant discovery (e.g. mapping of exome capture), and re-sequencing (mapping of WGS reads).
|
|
http://www.w3.org/1999/02/22-rdf-syntax-ns#type
|
http://www.w3.org/2002/07/owl#Class
|
|
http://www.w3.org/2000/01/rdf-schema#comment
|
This includes resources that aim to identify, map or analyse genetic markers in DNA sequences, for example to produce a genetic (linkage) map of a chromosome or genome or to analyse genetic linkage and synteny. It also includes resources for physical (sequence) maps of a DNA sequence showing the physical distance (base pairs) between features or landmarks such as restriction sites, cloned DNA fragments, genes and other genetic markers. It also covers for example the alignment of sequences of (typically millions) of short reads to a reference genome.
|
|
http://www.w3.org/2000/01/rdf-schema#subClassOf
|
http://edamontology.org/topic_0080
|
|
http://www.geneontology.org/formats/oboInOwl#hasHumanReadableId
|
Mapping
|
http://edamontology.org/topic_0196 |
|
http://www.geneontology.org/formats/oboInOwl#inSubset
|
http://purl.obolibrary.org/obo/edam#topics |
| http://purl.obolibrary.org/obo/edam#edam
|
|
http://edamontology.org/isdebtag
|
true
|
|
http://www.w3.org/2000/01/rdf-schema#label
|
Sequence assembly
|
|
http://edamontology.org/created_in
|
beta12orEarlier
|
|
http://www.geneontology.org/formats/oboInOwl#hasNarrowSynonym
|
Assembly
|
|
http://www.w3.org/2000/01/rdf-schema#seeAlso
|
https://en.wikipedia.org/wiki/Sequence_assembly
|
|
http://www.geneontology.org/formats/oboInOwl#hasDefinition
|
The assembly of fragments of a DNA sequence to reconstruct the original sequence.
|
|
http://www.w3.org/1999/02/22-rdf-syntax-ns#type
|
http://www.w3.org/2002/07/owl#Class
|
|
http://www.w3.org/2000/01/rdf-schema#comment
|
Assembly has two broad types, de-novo and re-sequencing. Re-sequencing is a specialised case of assembly, where an assembled (typically de-novo assembled) reference genome is available and is about 95% identical to the re-sequenced genome. All other cases of assembly are 'de-novo'.
|
|
http://www.w3.org/2000/01/rdf-schema#subClassOf
|
http://edamontology.org/topic_0080
|
|
http://www.geneontology.org/formats/oboInOwl#hasHumanReadableId
|
Sequence_assembly
|
http://edamontology.org/topic_0176 |
|
http://www.geneontology.org/formats/oboInOwl#inSubset
|
http://purl.obolibrary.org/obo/edam#topics |
| http://purl.obolibrary.org/obo/edam#edam
|
|
http://edamontology.org/isdebtag
|
true
|
|
http://www.w3.org/2000/01/rdf-schema#label
|
Molecular dynamics
|
|
http://edamontology.org/created_in
|
beta12orEarlier
|
|
http://www.geneontology.org/formats/oboInOwl#hasNarrowSynonym
|
Protein dynamics
|
|
http://www.w3.org/2000/01/rdf-schema#seeAlso
|
https://en.wikipedia.org/wiki/Molecular_dynamics
|
|
http://www.geneontology.org/formats/oboInOwl#hasDefinition
|
The study and simulation of molecular (typically protein) conformation using a computational model of physical forces and computer simulation.
|
|
http://www.w3.org/1999/02/22-rdf-syntax-ns#type
|
http://www.w3.org/2002/07/owl#Class
|
|
http://www.w3.org/2000/01/rdf-schema#comment
|
This includes methods such as Molecular Dynamics, Coarse-grained dynamics, metadynamics, Quantum Mechanics, QM/MM, Markov State Models, etc. This includes resources concerning flexibility and motion in protein and other molecular structures.
|
|
http://www.w3.org/2000/01/rdf-schema#subClassOf
|
http://edamontology.org/topic_0082 |
| http://edamontology.org/topic_3892
|
|
http://www.geneontology.org/formats/oboInOwl#hasHumanReadableId
|
Molecular_dynamics
|
|
http://www.geneontology.org/formats/oboInOwl#hasBroadSynonym
|
Molecular flexibility |
| Molecular motions
|
http://edamontology.org/topic_0154 |
|
http://www.geneontology.org/formats/oboInOwl#inSubset
|
http://purl.obolibrary.org/obo/edam#topics |
| http://purl.obolibrary.org/obo/edam#edam
|
|
http://edamontology.org/isdebtag
|
true
|
|
http://www.w3.org/2000/01/rdf-schema#label
|
Small molecules
|
|
http://edamontology.org/created_in
|
beta12orEarlier
|
|
http://www.geneontology.org/formats/oboInOwl#hasNarrowSynonym
|
Toxins and targets |
| Toxins |
| Peptides and amino acids |
| Targets |
| Drug structures |
| Chemical structures |
| Metabolite structures |
| Drug targets |
| Peptides |
| Amino acids |
| Target structures |
| Drugs and target structures
|
|
http://www.w3.org/2000/01/rdf-schema#seeAlso
|
https://en.wikipedia.org/wiki/Small_molecule |
| https://en.wikipedia.org/wiki/Metabolite
|
|
http://www.geneontology.org/formats/oboInOwl#hasDefinition
|
Small molecules of biological significance, typically archival, curation, processing and analysis of structural information.
|
|
http://www.w3.org/1999/02/22-rdf-syntax-ns#type
|
http://www.w3.org/2002/07/owl#Class
|
|
http://www.w3.org/2000/01/rdf-schema#comment
|
This concept excludes macromolecules such as proteins and nucleic acids. |
| Small molecules include organic molecules, metal-organic compounds, small polypeptides, small polysaccharides and oligonucleotides. Structural data is usually included. |
| This includes the structures of drugs, drug target, their interactions and binding affinities. Also the structures of reactants or products of metabolism, for example small molecules such as including vitamins, polyols, nucleotides and amino acids. Also the physicochemical, biochemical or structural properties of amino acids or peptides. Also structural and associated data for toxic chemical substances.
|
|
http://www.geneontology.org/formats/oboInOwl#hasHumanReadableId
|
Small_molecules
|
|
http://www.w3.org/2000/01/rdf-schema#subClassOf
|
http://edamontology.org/topic_0081
|
|
http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym
|
CHEBI:23367
|
http://edamontology.org/topic_0157 |
|
http://www.geneontology.org/formats/oboInOwl#inSubset
|
http://purl.obolibrary.org/obo/edam#topics |
| http://purl.obolibrary.org/obo/edam#edam
|
|
http://edamontology.org/isdebtag
|
true
|
|
http://www.w3.org/2000/01/rdf-schema#label
|
Sequence composition, complexity and repeats
|
|
http://edamontology.org/created_in
|
beta12orEarlier
|
|
http://www.geneontology.org/formats/oboInOwl#hasNarrowSynonym
|
Protein sequence repeats |
| Repeat sequences |
| Sequence repeats |
| Protein repeats |
| Sequence composition |
| Sequence complexity |
| Low complexity sequences |
| Nucleic acid repeats
|
|
http://www.geneontology.org/formats/oboInOwl#hasDefinition
|
The archival, processing and analysis of the basic character composition of molecular sequences, for example character or word frequency, ambiguity, complexity, particularly regions of low complexity, and repeats or the repetitive nature of molecular sequences.
|
|
http://www.w3.org/1999/02/22-rdf-syntax-ns#type
|
http://www.w3.org/2002/07/owl#Class
|
|
http://www.w3.org/2000/01/rdf-schema#comment
|
This includes short repetitive subsequences (repeat sequences) in a protein sequence. |
| This includes repetitive elements within a nucleic acid sequence, e.g. long terminal repeats (LTRs); sequences (typically retroviral) directly repeated at both ends of a sequence and other types of repeating unit.
|
|
http://www.w3.org/2000/01/rdf-schema#subClassOf
|
http://edamontology.org/topic_0080
|
|
http://www.geneontology.org/formats/oboInOwl#hasHumanReadableId
|
Sequence_composition_complexity_and_repeats
|
http://edamontology.org/topic_0160 |
|
http://www.geneontology.org/formats/oboInOwl#inSubset
|
http://purl.obolibrary.org/obo/edam#topics |
| http://purl.obolibrary.org/obo/edam#edam
|
|
http://edamontology.org/isdebtag
|
true
|
|
http://www.w3.org/2000/01/rdf-schema#label
|
Sequence sites, features and motifs
|
|
http://edamontology.org/created_in
|
beta12orEarlier
|
|
http://www.geneontology.org/formats/oboInOwl#hasNarrowSynonym
|
Sequence profiles |
| HMMs |
| Sequence features |
| Sequence motifs |
| Functional sites |
| Sequence sites
|
|
http://www.geneontology.org/formats/oboInOwl#hasDefinition
|
The archival, detection, prediction and analysis of positional features such as functional and other key sites, in molecular sequences and the conserved patterns (motifs, profiles etc.) that may be used to describe them.
|
|
http://www.w3.org/1999/02/22-rdf-syntax-ns#type
|
http://www.w3.org/2002/07/owl#Class
|
|
http://www.w3.org/2000/01/rdf-schema#subClassOf
|
http://edamontology.org/topic_3307
|
|
http://www.geneontology.org/formats/oboInOwl#hasHumanReadableId
|
Sequence_sites_features_and_motifs
|
http://edamontology.org/topic_0166 |
|
http://www.geneontology.org/formats/oboInOwl#inSubset
|
http://purl.obolibrary.org/obo/edam#topics |
| http://purl.obolibrary.org/obo/edam#edam
|
|
http://edamontology.org/isdebtag
|
true
|
|
http://www.w3.org/2000/01/rdf-schema#label
|
Protein structural motifs and surfaces
|
|
http://edamontology.org/created_in
|
beta12orEarlier
|
|
http://www.geneontology.org/formats/oboInOwl#hasNarrowSynonym
|
Protein structural motifs |
| Protein surfaces |
| Protein structural features |
| Structural motifs
|
|
http://www.geneontology.org/formats/oboInOwl#hasDefinition
|
Structural features or common 3D motifs within protein structures, including the surface of a protein structure, such as biological interfaces with other molecules.
|
|
http://www.w3.org/1999/02/22-rdf-syntax-ns#type
|
http://www.w3.org/2002/07/owl#Class
|
|
http://www.geneontology.org/formats/oboInOwl#hasExactSynonym
|
Protein 3D motifs
|
|
http://www.w3.org/2000/01/rdf-schema#comment
|
This includes conformation of conserved substructures, conserved geometry (spatial arrangement) of secondary structure or protein backbone, solvent-exposed surfaces, internal cavities, the analysis of shape, hydropathy, electrostatic patches, role and functions etc.
|
|
http://www.w3.org/2000/01/rdf-schema#subClassOf
|
http://edamontology.org/topic_2814
|
|
http://www.geneontology.org/formats/oboInOwl#hasHumanReadableId
|
Protein_structural_motifs_and_surfaces
|
http://edamontology.org/topic_0130 |
|
http://www.geneontology.org/formats/oboInOwl#inSubset
|
http://purl.obolibrary.org/obo/edam#topics |
| http://purl.obolibrary.org/obo/edam#edam
|
|
http://edamontology.org/isdebtag
|
true
|
|
http://www.w3.org/2000/01/rdf-schema#label
|
Protein folding, stability and design
|
|
http://edamontology.org/created_in
|
beta12orEarlier
|
|
http://www.geneontology.org/formats/oboInOwl#hasNarrowSynonym
|
Protein folding |
| Protein residue interactions |
| Protein design |
| Rational protein design |
| Protein stability
|
|
http://www.w3.org/2000/01/rdf-schema#seeAlso
|
https://en.wikipedia.org/wiki/Protein_folding |
| https://en.wikipedia.org/wiki/Protein_design
|
|
http://www.geneontology.org/formats/oboInOwl#hasDefinition
|
Protein stability, folding (in 3D space) and protein sequence-structure-function relationships. This includes for example study of inter-atomic or inter-residue interactions in protein (3D) structures, the effect of mutation, and the design of proteins with specific properties, typically by designing changes (via site-directed mutagenesis) to an existing protein.
|
|
http://www.w3.org/1999/02/22-rdf-syntax-ns#type
|
http://www.w3.org/2002/07/owl#Class
|
|
http://www.w3.org/2000/01/rdf-schema#subClassOf
|
http://edamontology.org/topic_2814
|
|
http://www.geneontology.org/formats/oboInOwl#hasHumanReadableId
|
Protein_folding_stability_and_design
|
http://edamontology.org/topic_3295 |
|
http://www.geneontology.org/formats/oboInOwl#inSubset
|
http://purl.obolibrary.org/obo/edam#events |
| http://purl.obolibrary.org/obo/edam#topics |
| http://purl.obolibrary.org/obo/edam#edam
|
|
http://edamontology.org/isdebtag
|
true
|
|
http://www.w3.org/2000/01/rdf-schema#label
|
Epigenetics
|
|
http://edamontology.org/created_in
|
1.3
|
|
http://www.geneontology.org/formats/oboInOwl#hasNarrowSynonym
|
Histone modification |
| DNA methylation
|
|
http://www.w3.org/2000/01/rdf-schema#seeAlso
|
http://purl.bioontology.org/ontology/MSH/D019175 |
| https://en.wikipedia.org/wiki/Epigenetics
|
|
http://www.geneontology.org/formats/oboInOwl#hasDefinition
|
Topic concerning the study of heritable changes, for example in gene expression or phenotype, caused by mechanisms other than changes in the DNA sequence.
|
|
http://www.w3.org/1999/02/22-rdf-syntax-ns#type
|
http://www.w3.org/2002/07/owl#Class
|
|
http://www.w3.org/2000/01/rdf-schema#comment
|
This includes sub-topics such as histone modification and DNA methylation (methylation sites and analysis, for example of patterns and profiles of DNA methylation in a population, tissue etc.)
|
|
http://www.w3.org/2000/01/rdf-schema#subClassOf
|
http://edamontology.org/topic_3053
|
|
http://www.geneontology.org/formats/oboInOwl#hasHumanReadableId
|
Epigenetics
|
http://edamontology.org/operation_0253 |
|
http://www.geneontology.org/formats/oboInOwl#inSubset
|
http://purl.obolibrary.org/obo/edam#edam |
| http://purl.obolibrary.org/obo/edam#operations
|
|
http://www.w3.org/2000/01/rdf-schema#label
|
Sequence feature detection
|
|
http://edamontology.org/created_in
|
beta12orEarlier
|
|
http://www.geneontology.org/formats/oboInOwl#hasNarrowSynonym
|
Motif database search
|
|
http://www.geneontology.org/formats/oboInOwl#hasDefinition
|
Predict, recognise and identify positional features in molecular sequences such as key functional sites or regions.
|
|
http://www.w3.org/1999/02/22-rdf-syntax-ns#type
|
http://www.w3.org/2002/07/owl#Class
|
|
http://www.geneontology.org/formats/oboInOwl#hasExactSynonym
|
Sequence feature prediction |
| Sequence feature recognition
|
|
http://www.w3.org/2000/01/rdf-schema#comment
|
Look at "Protein feature detection" (http://edamontology.org/operation_3092) and "Nucleic acid feature detection" (http://edamontology.org/operation_0415) in case more specific terms are needed.
|
|
http://www.w3.org/2000/01/rdf-schema#subClassOf
|
_:575 |
| http://edamontology.org/operation_2403 |
| http://edamontology.org/operation_2423 |
| _:574
|
|
http://www.geneontology.org/formats/oboInOwl#hasRelatedSynonym
|
SO:0000110
|
http://edamontology.org/operation_0252 |
|
http://www.geneontology.org/formats/oboInOwl#inSubset
|
http://purl.obolibrary.org/obo/edam#edam |
| http://purl.obolibrary.org/obo/edam#operations
|
|
http://www.w3.org/2000/01/rdf-schema#label
|
Peptide immunogenicity prediction
|
|
http://edamontology.org/created_in
|
beta12orEarlier
|
|
http://www.geneontology.org/formats/oboInOwl#hasNarrowSynonym
|
Hopp and Woods plotting |
| MHC peptide immunogenicity prediction
|
|
http://www.geneontology.org/formats/oboInOwl#hasDefinition
|
Predict antigenicity, allergenicity / immunogenicity, allergic cross-reactivity etc of peptides and proteins.
|
|
http://www.w3.org/1999/02/22-rdf-syntax-ns#type
|
http://www.w3.org/2002/07/owl#Class
|
|
http://www.geneontology.org/formats/oboInOwl#hasExactSynonym
|
Immunogenicity prediction
|
|
http://www.w3.org/2000/01/rdf-schema#comment
|
This includes methods that generate a graphical rendering of antigenicity of a protein, such as a Hopp and Woods plot. |
| This is usually done in the development of peptide-specific antibodies or multi-epitope vaccines. Methods might use sequence data (for example motifs) and / or structural data.
|
|
http://www.w3.org/2000/01/rdf-schema#subClassOf
|
_:365 |
| http://edamontology.org/operation_1777 |
| http://edamontology.org/operation_0250 |
| _:415
|
http://edamontology.org/topic_2818 |
|
http://www.geneontology.org/formats/oboInOwl#inSubset
|
http://purl.obolibrary.org/obo/edam#obsolete
|
|
http://www.w3.org/2002/07/owl#deprecated
|
true
|
|
http://www.w3.org/2000/01/rdf-schema#label
|
Eukaryotes
|
|
http://edamontology.org/created_in
|
beta12orEarlier
|
|
http://www.geneontology.org/formats/oboInOwl#hasDefinition
|
Eukaryotes or data concerning eukaryotes, e.g. information on a specific eukaryote genome including molecular sequences, genes and annotation.
|
|
http://edamontology.org/deprecation_comment
|
(jison) Out of EDAM scope. While very useful to have a basic set of IDs for organisms, should find a better way to provide this e.g. in bio.tools (NCBI taxon ID subset).
|
|
http://www.geneontology.org/formats/oboInOwl#consider
|
http://edamontology.org/topic_0621
|
|
http://www.w3.org/1999/02/22-rdf-syntax-ns#type
|
http://www.w3.org/2002/07/owl#Class
|
|
http://www.w3.org/2000/01/rdf-schema#comment
|
The resource may be specific to a eukaryote, a group of eukaryotes or all eukaryotes.
|
|
http://www.w3.org/2000/01/rdf-schema#subClassOf
|
http://www.w3.org/2002/07/owl#DeprecatedClass
|
|
http://edamontology.org/oldParent
|
http://edamontology.org/topic_0621
|
|
http://edamontology.org/obsolete_since
|
1.17
|
http://edamontology.org/operation_0250 |
|
http://www.geneontology.org/formats/oboInOwl#inSubset
|
http://purl.obolibrary.org/obo/edam#edam |
| http://purl.obolibrary.org/obo/edam#operations
|
|
http://www.w3.org/2000/01/rdf-schema#label
|
Protein property calculation
|
|
http://edamontology.org/created_in
|
beta12orEarlier
|
|
http://www.geneontology.org/formats/oboInOwl#hasNarrowSynonym
|
Protein property calculation (from structure) |
| Protein structural property calculation |
| Protein property calculation (from sequence)
|
|
http://www.geneontology.org/formats/oboInOwl#hasDefinition
|
Extract, calculate or predict non-positional (physical or chemical) properties of a protein, including any non-positional properties of the molecular sequence, from processing a protein sequence or 3D structure.
|
|
http://www.w3.org/1999/02/22-rdf-syntax-ns#type
|
http://www.w3.org/2002/07/owl#Class
|
|
http://www.geneontology.org/formats/oboInOwl#hasExactSynonym
|
Protein property rendering
|
|
http://www.w3.org/2000/01/rdf-schema#comment
|
This includes methods to render and visualise the properties of a protein sequence, and a residue-level search for properties such as solvent accessibility, hydropathy, secondary structure, ligand-binding etc.
|
|
http://www.w3.org/2000/01/rdf-schema#subClassOf
|
http://edamontology.org/operation_2423 |
| http://edamontology.org/operation_3438
|
http://edamontology.org/operation_0267 |
|
http://www.geneontology.org/formats/oboInOwl#inSubset
|
http://purl.obolibrary.org/obo/edam#edam |
| http://purl.obolibrary.org/obo/edam#operations
|
|
http://www.w3.org/2000/01/rdf-schema#label
|
Protein secondary structure prediction
|
|
http://edamontology.org/created_in
|
beta12orEarlier
|
|
http://www.geneontology.org/formats/oboInOwl#hasDefinition
|
Predict secondary structure of protein sequences.
|
|
http://www.w3.org/1999/02/22-rdf-syntax-ns#type
|
http://www.w3.org/2002/07/owl#Class
|
|
http://www.geneontology.org/formats/oboInOwl#hasExactSynonym
|
Secondary structure prediction (protein)
|
|
http://www.w3.org/2000/01/rdf-schema#comment
|
Methods might use amino acid composition, local sequence information, multiple sequence alignments, physicochemical features, estimated energy content, statistical algorithms, hidden Markov models, support vector machines, kernel machines, neural networks etc.
|
|
http://www.w3.org/2000/01/rdf-schema#subClassOf
|
http://edamontology.org/operation_2479 |
| http://edamontology.org/operation_2423 |
| http://edamontology.org/operation_2416 |
| http://edamontology.org/operation_3092
|
http://edamontology.org/topic_2820 |
|
http://www.geneontology.org/formats/oboInOwl#inSubset
|
http://purl.obolibrary.org/obo/edam#obsolete
|
|
http://www.w3.org/2002/07/owl#deprecated
|
true
|
|
http://www.w3.org/2000/01/rdf-schema#label
|
Vertebrates
|
|
http://edamontology.org/created_in
|
beta12orEarlier
|
|
http://edamontology.org/deprecation_comment
|
(jison)Out of EDAM scope. While very useful to have a basic set of IDs for organisms, should find a better way to provide this e.g. in bio.tools (NCBI taxon ID subset).
|
|
http://www.geneontology.org/formats/oboInOwl#hasDefinition
|
Vertebrates, e.g. information on a specific vertebrate genome including molecular sequences, genes and annotation.
|
|
http://www.geneontology.org/formats/oboInOwl#consider
|
http://edamontology.org/topic_0621
|
|
http://www.w3.org/1999/02/22-rdf-syntax-ns#type
|
http://www.w3.org/2002/07/owl#Class
|
|
http://www.w3.org/2000/01/rdf-schema#comment
|
The resource may be specific to a vertebrate, a group of vertebrates or all vertebrates.
|
|
http://www.w3.org/2000/01/rdf-schema#subClassOf
|
http://www.w3.org/2002/07/owl#DeprecatedClass
|
|
http://edamontology.org/oldParent
|
http://edamontology.org/topic_3500
|
|
http://edamontology.org/obsolete_since
|
1.17
|
http://edamontology.org/data_0954 |
|
http://www.geneontology.org/formats/oboInOwl#inSubset
|
http://purl.obolibrary.org/obo/edam#edam |
| http://purl.obolibrary.org/obo/edam#data
|
|
http://www.w3.org/2000/01/rdf-schema#label
|
Database cross-mapping
|
|
http://edamontology.org/created_in
|
beta12orEarlier
|
|
http://www.geneontology.org/formats/oboInOwl#hasDefinition
|
A mapping of the accession numbers (or other database identifier) of entries between (typically) two biological or biomedical databases.
|
|
http://www.w3.org/1999/02/22-rdf-syntax-ns#type
|
http://www.w3.org/2002/07/owl#Class
|
|
http://www.w3.org/2000/01/rdf-schema#comment
|
The cross-mapping is typically a table where each row is an accession number and each column is a database being cross-referenced. The cells give the accession number or identifier of the corresponding entry in a database. If a cell in the table is not filled then no mapping could be found for the database. Additional information might be given on version, date etc.
|
|
http://www.w3.org/2000/01/rdf-schema#subClassOf
|
http://edamontology.org/data_2093
|
http://edamontology.org/operation_0237 |
|
http://www.geneontology.org/formats/oboInOwl#inSubset
|
http://purl.obolibrary.org/obo/edam#edam |
| http://purl.obolibrary.org/obo/edam#operations
|
|
http://www.w3.org/2000/01/rdf-schema#label
|
Repeat sequence analysis
|
|
http://edamontology.org/created_in
|
beta12orEarlier
|
|
http://www.geneontology.org/formats/oboInOwl#hasDefinition
|
Find and/or analyse repeat sequences in (typically nucleotide) sequences.
|
|
http://www.w3.org/1999/02/22-rdf-syntax-ns#type
|
http://www.w3.org/2002/07/owl#Class
|
|
http://www.w3.org/2000/01/rdf-schema#comment
|
Repeat sequences include tandem repeats, inverted or palindromic repeats, DNA microsatellites (Simple Sequence Repeats or SSRs), interspersed repeats, maximal duplications and reverse, complemented and reverse complemented repeats etc. Repeat units can be exact or imperfect, in tandem or dispersed, of specified or unspecified length.
|
|
http://www.w3.org/2000/01/rdf-schema#subClassOf
|
http://edamontology.org/operation_2403 |
| _:511
|
http://edamontology.org/operation_0244 |
|
http://www.geneontology.org/formats/oboInOwl#inSubset
|
http://purl.obolibrary.org/obo/edam#edam |
| http://purl.obolibrary.org/obo/edam#operations
|
|
http://www.w3.org/2000/01/rdf-schema#label
|
Simulation analysis
|
|
http://edamontology.org/created_in
|
beta12orEarlier
|
|
http://www.geneontology.org/formats/oboInOwl#hasNarrowSynonym
|
Protein flexibility prediction |
| Protein flexibility and motion analysis |
| Nucleic Acid Dynamics Analysis |
| Protein motion prediction
|
|
http://www.geneontology.org/formats/oboInOwl#hasDefinition
|
Analyse flexibility and motion in protein structure.
|
|
http://www.w3.org/1999/02/22-rdf-syntax-ns#type
|
http://www.w3.org/2002/07/owl#Class
|
|
http://www.geneontology.org/formats/oboInOwl#hasExactSynonym
|
CG analysis |
| Protein Dynamics Analysis |
| Trajectory analysis |
| MD analysis
|
|
http://www.w3.org/2000/01/rdf-schema#comment
|
Use this concept for analysis of flexible and rigid residues, local chain deformability, regions undergoing conformational change, molecular vibrations or fluctuational dynamics, domain motions or other large-scale structural transitions in a protein structure.
|
|
http://www.w3.org/2000/01/rdf-schema#subClassOf
|
http://edamontology.org/operation_0250
|
http://edamontology.org/operation_0248 |
|
http://www.geneontology.org/formats/oboInOwl#inSubset
|
http://purl.obolibrary.org/obo/edam#edam |
| http://purl.obolibrary.org/obo/edam#operations
|
|
http://www.geneontology.org/formats/oboInOwl#hasDbXref
|
WHATIF: SymShellTwoXML |
| WHATIF: SymShellFiveXML |
| WHATIF:ListContactsRelaxed |
| WHATIF: SymShellOneXML |
| WHATIF:ListSideChainContactsNormal |
| WHATIF:ListContactsNormal |
| WHATIF:ListSideChainContactsRelaxed |
| WHATIF: SymShellTenXML
|
|
http://www.w3.org/2000/01/rdf-schema#label
|
Residue interaction calculation
|
|
http://edamontology.org/created_in
|
beta12orEarlier
|
|
http://www.geneontology.org/formats/oboInOwl#hasDefinition
|
Calculate or extract inter-atomic, inter-residue or residue-atom contacts, distances and interactions in protein structure(s).
|
|
http://www.w3.org/1999/02/22-rdf-syntax-ns#type
|
http://www.w3.org/2002/07/owl#Class
|
|
http://www.w3.org/2000/01/rdf-schema#subClassOf
|
_:593 |
| http://edamontology.org/operation_0250
|
http://edamontology.org/data_0976 |
|
http://www.geneontology.org/formats/oboInOwl#inSubset
|
http://purl.obolibrary.org/obo/edam#edam |
| http://purl.obolibrary.org/obo/edam#data |
| http://purl.obolibrary.org/obo/edam#identifiers
|
|
http://edamontology.org/notRecommendedForAnnotation
|
true
|
|
http://www.w3.org/2000/01/rdf-schema#label
|
Identifier (by type of data)
|
|
http://edamontology.org/created_in
|
beta12orEarlier
|
|
http://www.geneontology.org/formats/oboInOwl#hasDefinition
|
An identifier that identifies a particular type of data.
|
|
http://www.w3.org/1999/02/22-rdf-syntax-ns#type
|
http://www.w3.org/2002/07/owl#Class
|
|
http://www.geneontology.org/formats/oboInOwl#hasExactSynonym
|
Identifier (typed)
|
|
http://www.w3.org/2000/01/rdf-schema#comment
|
This concept exists only to assist EDAM maintenance and navigation in graphical browsers. It does not add semantic information. This branch provides an alternative organisation of the concepts nested under 'Accession' and 'Name'. All concepts under here are already included under 'Accession' or 'Name'.
|
|
http://www.w3.org/2000/01/rdf-schema#subClassOf
|
http://edamontology.org/data_0842
|
http://edamontology.org/operation_0295 |
|
http://www.geneontology.org/formats/oboInOwl#inSubset
|
http://purl.obolibrary.org/obo/edam#edam |
| http://purl.obolibrary.org/obo/edam#operations
|
|
http://www.geneontology.org/formats/oboInOwl#comment
|
Includes methods that align structural (3D) profiles or templates (representing structures or structure alignments) - including methods that perform one-to-one, one-to-many or many-to-many comparisons.
|
|
http://www.w3.org/2000/01/rdf-schema#label
|
Structure alignment
|
|
http://edamontology.org/created_in
|
beta12orEarlier
|
|
http://www.geneontology.org/formats/oboInOwl#hasNarrowSynonym
|
3D profile-to-3D profile alignment |
| 3D profile alignment |
| Structural profile alignment
|
|
http://www.w3.org/2000/01/rdf-schema#seeAlso
|
https://en.wikipedia.org/wiki/Structural_alignment
|
|
http://www.geneontology.org/formats/oboInOwl#hasDefinition
|
Align (superimpose) molecular tertiary structures.
|
|
http://www.w3.org/1999/02/22-rdf-syntax-ns#type
|
http://www.w3.org/2002/07/owl#Class
|
|
http://www.geneontology.org/formats/oboInOwl#hasExactSynonym
|
Structural alignment
|
|
http://www.w3.org/2000/01/rdf-schema#subClassOf
|
_:412 |
| http://edamontology.org/operation_2928 |
| http://edamontology.org/operation_2483 |
| http://edamontology.org/operation_2480
|
http://edamontology.org/operation_0292 |
|
http://www.geneontology.org/formats/oboInOwl#inSubset
|
http://purl.obolibrary.org/obo/edam#edam |
| http://purl.obolibrary.org/obo/edam#operations
|
|
http://www.geneontology.org/formats/oboInOwl#comment
|
Includes methods that align sequence profiles (representing sequence alignments): ethods might perform one-to-one, one-to-many or many-to-many comparisons. See also 'Sequence alignment comparison'.
|
|
http://www.w3.org/2000/01/rdf-schema#label
|
Sequence alignment
|
|
http://edamontology.org/created_in
|
beta12orEarlier
|
|
http://www.geneontology.org/formats/oboInOwl#hasNarrowSynonym
|
Constrained sequence alignment |
| Sequence alignment (constrained) |
| Multiple sequence alignment (constrained) |
| Consensus-based sequence alignment
|
|
http://www.w3.org/2000/01/rdf-schema#seeAlso
|
https://en.wikipedia.org/wiki/Sequence_alignment
|
|
http://www.geneontology.org/formats/oboInOwl#hasDefinition
|
Align (identify equivalent sites within) molecular sequences.
|
|
http://www.w3.org/1999/02/22-rdf-syntax-ns#type
|
http://www.w3.org/2002/07/owl#Class
|
|
http://www.geneontology.org/formats/oboInOwl#hasExactSynonym
|
Sequence alignment construction |
| Sequence alignment generation
|
|
http://www.w3.org/2000/01/rdf-schema#subClassOf
|
http://edamontology.org/operation_2451 |
| http://edamontology.org/operation_2403 |
| _:357 |
| http://edamontology.org/operation_2928
|
http://edamontology.org/operation_0279 |
|
http://www.geneontology.org/formats/oboInOwl#inSubset
|
http://purl.obolibrary.org/obo/edam#edam |
| http://purl.obolibrary.org/obo/edam#operations
|
|
http://www.w3.org/2000/01/rdf-schema#label
|
Nucleic acid folding analysis
|
|
http://edamontology.org/created_in
|
beta12orEarlier
|
|
http://www.geneontology.org/formats/oboInOwl#hasNarrowSynonym
|
Nucleic acid folding energy calculation
|
|
http://www.geneontology.org/formats/oboInOwl#hasDefinition
|
Analyse some aspect of RNA/DNA folding, typically by processing sequence and/or structural data. For example, compute folding energies such as minimum folding energies for DNA or RNA sequences or energy landscape of RNA mutants.
|
|
http://www.w3.org/1999/02/22-rdf-syntax-ns#type
|
http://www.w3.org/2002/07/owl#Class
|
|
http://www.geneontology.org/formats/oboInOwl#hasExactSynonym
|
Nucleic acid folding prediction |
| Nucleic acid folding modelling |
| Nucleic acid folding
|
|
http://www.w3.org/2000/01/rdf-schema#subClassOf
|
http://edamontology.org/operation_0475 |
| http://edamontology.org/operation_2426 |
| _:595 |
| http://edamontology.org/operation_2481
|
http://edamontology.org/operation_0270 |
|
http://www.geneontology.org/formats/oboInOwl#inSubset
|
http://purl.obolibrary.org/obo/edam#edam |
| http://purl.obolibrary.org/obo/edam#operations
|
|
http://www.w3.org/2000/01/rdf-schema#label
|
Transmembrane protein analysis
|
|
http://edamontology.org/created_in
|
beta12orEarlier
|
|
http://www.geneontology.org/formats/oboInOwl#hasDefinition
|
Analyse transmembrane protein(s), typically by processing sequence and / or structural data, and write an informative report for example about the protein and its transmembrane domains / regions.
|
|
http://www.w3.org/1999/02/22-rdf-syntax-ns#type
|
http://www.w3.org/2002/07/owl#Class
|
|
http://www.w3.org/2000/01/rdf-schema#comment
|
Use this (or child) concept for analysis of transmembrane domains (buried and exposed faces), transmembrane helices, helix topology, orientation, inter-helical contacts, membrane dipping (re-entrant) loops and other secondary structure etc. Methods might use pattern discovery, hidden Markov models, sequence alignment, structural profiles, amino acid property analysis, comparison to known domains or some combination (hybrid methods).
|
|
http://www.w3.org/2000/01/rdf-schema#subClassOf
|
_:252 |
| http://edamontology.org/operation_2945
|
http://edamontology.org/operation_0282 |
|
http://www.geneontology.org/formats/oboInOwl#inSubset
|
http://purl.obolibrary.org/obo/edam#edam |
| http://purl.obolibrary.org/obo/edam#operations
|
|
http://www.w3.org/2000/01/rdf-schema#label
|
Genetic mapping
|
|
http://edamontology.org/created_in
|
beta12orEarlier
|
|
http://www.geneontology.org/formats/oboInOwl#hasNarrowSynonym
|
QTL mapping
|
|
http://www.w3.org/2000/01/rdf-schema#seeAlso
|
https://en.wikipedia.org/wiki/Gene_mapping#Gene_mapping
|
|
http://www.geneontology.org/formats/oboInOwl#hasDefinition
|
Generate a genetic (linkage) map of a DNA sequence (typically a chromosome) showing the relative positions of genetic markers based on estimation of non-physical distances.
|
|
http://www.w3.org/1999/02/22-rdf-syntax-ns#type
|
http://www.w3.org/2002/07/owl#Class
|
|
http://www.geneontology.org/formats/oboInOwl#hasExactSynonym
|
Genetic map construction |
| Functional mapping |
| Genetic map generation |
| Linkage mapping
|
|
http://www.w3.org/2000/01/rdf-schema#comment
|
This includes mapping of the genetic architecture of dynamic complex traits (functional mapping), e.g. by characterisation of the underlying quantitative trait loci (QTLs) or nucleotides (QTNs). |
| Mapping involves ordering genetic loci along a chromosome and estimating the physical distance between loci. A genetic map shows the relative (not physical) position of known genes and genetic markers.
|
|
http://www.w3.org/2000/01/rdf-schema#subClassOf
|
http://edamontology.org/operation_2520 |
| _:446 |
| http://edamontology.org/operation_3429
|