emboss-test 6.4.0-2 / usr / share / EMBOSS / test / data / EDAM.obo

format-version: 1.2
date: 01:12:2010 12:25
data-version: Beta12
! Use for mapping to "global" id space(s) e.g.:
! idspace: EDAM http://purl.org/edam/ "EDAM terms"
! NEXT term number is 0002891
! xref: WHATIF: CorrectedPDBasXML
! xref:http://www.geneontology.org/doc/GO.xrf_abbs: FB
! xref:Moby:GI_Gene ! xref: Moby_namespace:iHOPorganism
! xref: SO:0000348
! xref: BioCatalogue:Protein Multiple Alignment
! xref: GO:0006464 ! protein modification process
! regex: Regular expression for validating a "data<-identifier" instance.
! spec_url: URL of format specification for a "format" term
! seealso: Ontology term ID of term in external ontology for fine-grained annotation



!
! EDAM relations
!
[Typedef]
id: concerns
name: concerns
def: "Defines that a term ('Topic') concerns (covers) another term ('Data', 'Resource' or 'Operation')." [EDAM:EBI]
is_anti_symmetric: true
is_cyclic: false
is_transitive: true
! inverse_of: is_concern_of

! [Typedef]
! id: has_attribute
! name: has_attribute
! def: "Defines a term ('Biological entity') has (or can have) an attribute ('Data')." [EDAM:EBI]
! is_anti_symmetric: true
! is_cyclic: false
! is_transitive: true
! inverse_of: is_attribute_of

! [Typedef]
! id: has_identifier
! name: has_identifier
! def: "Defines a term ('Biological entity', 'Resource' or 'Data') has (or can have) an identifier ('Identifier')." [EDAM:EBI]
! is_anti_symmetric: true
! is_cyclic: false
! is_transitive: true
! inverse_of: is_identifier_of

[Typedef]
id: has_input
name: has_input
def: "Defines a term ('Operation') as necessarily consuming another term ('Data') as input." [EDAM:EBI]
is_anti_symmetric: true
is_cyclic: false
is_transitive: true
! inverse_of: is_input_of

[Typedef]
id: has_output
name: has_output
def: "Defines a term ('Operation') as necessarily producing another term ('Data') as output." [EDAM:EBI]
is_anti_symmetric: true
is_cyclic: false
is_transitive: true
! inverse_of: is_output_of

! [Typedef]
! id: has_part
! name: has_part
! def: "Defines a term ('Biological entity' or 'Data') as having a conceptual part ('Biological entity' or 'Data')." [EDAM:EBI]
! is_anti_symmetric: true
! is_cyclic: false
! is_transitive: true
! inverse_of: is_part_of

! [Typedef]
! id: has_source
! name: has_source
! def: "Defines a term ('Data') has a source ('Operation', 'Resource')." [EDAM:EBI]
! comment: is_source_of
! is_anti_symmetric: true
! is_cyclic: false
! is_transitive: true
! inverse_of: is_source_of


! [Typedef]
! id: has_format
! name: has_format
! def: "Defines a term ('Data') has a data format specification ('Format')." [EDAM:EBI]
! is_anti_symmetric: true
! is_cyclic: false
! is_transitive: true
! inverse_of: is_format_of

! [Typedef]
! id: is_attribute_of
! name: is_attribute_of
! def: "Defines that a term ('Data') is an attribute of another term ('Biological entity')." [EDAM:EBI]
! is_anti_symmetric: true
! is_cyclic: false
! is_transitive: true
! inverse_of: has_attribute

! [Typedef]
! id: is_concern_of
! name: is_concern_of
! def: "Defines a term ('Biological entity', 'Resource' or 'Operation') as a concern of another term ('Topic')." [EDAM:EBI]
! is_anti_symmetric: true
! is_cyclic: false
! is_transitive: true
! inverse_of: concerns

[Typedef]
id: is_identifier_of
name: is_identifier_of
def: "Defines that a term ('Identifier') is an identifier of another term ('Resource' or 'Data')." [EDAM:EBI]
is_anti_symmetric: true
is_cyclic: false
is_transitive: true
! inverse_of: has_identifier

! [Typedef]
! id: is_input_of
! name: is_input_of
! def: "Defines a term ('Data') as an input of another term ('Operation')." [EDAM:EBI]
! is_anti_symmetric: true
! is_cyclic: false
! is_transitive: true
! inverse_of: has_input

! [Typedef]
! id: is_output_of
! name: is_output_of
! def: "Defines a term ('Data') as an output of another term ('Operation')." [EDAM:EBI]
! is_anti_symmetric: true
! is_cyclic: false
! is_transitive: true
! inverse_of: has_output

! [Typedef]
! id: is_part_of
! name: is_part_of
! def: "Defines that a term ('Biological entity' or 'Data') is a conceptual part of some other term ('Biological entity' or 'Data')." [EDAM:EBI]
! is_anti_symmetric: true
! is_cyclic: false
! is_transitive: true
! inverse_of: has_part

[Typedef]
id: is_source_of
name: is_source_of
def: "Defines a term ('Resource') is a source of another term ('Data')." [EDAM:EBI]
comment: has_source
is_anti_symmetric: true
is_cyclic: false
is_transitive: true
! inverse_of: has_source

[Typedef]
id: is_format_of
name: is_format_of
def: "Defines that a term ('Format') is a data format specification for another term ('Data')." [EDAM:EBI]
is_anti_symmetric: true
is_cyclic: false
is_transitive: true
! inverse_of: has_format




[Term]
id: EDAM:0000002
name: Biological entity
namespace: entity
def: Any biological thing (or part of a thing) with a physical existence, a physical part, region or feature that can be mapped to such a thing, a collection of such things or an observable phenonema or occurence.
is_obsolete: true

[Term]
id: EDAM:0000003
name: Topic
namespace: topic
def: A general field of bioinformatics study, data, processing and analysis or technology.

[Term]
id: EDAM:0000004
name: Operation
namespace: operation
def: A specific, singular function or process performed by a tool, for example a WS operation. What is done, but not (typically) how or in what context.

[Term]
id: EDAM:0000006
name: Data
namespace: data
def: A semantic description of a data entity (datum) commonly used in bioinformatics.

[Term]
id: EDAM:0000077
name: Nucleic acids
namespace: topic
def: Resources concerning nucleic acids.
is_a: EDAM:0000003 ! Topic
relationship: concerns EDAM:0002501 ! Nucleic acid data processing

[Term]
id: EDAM:0000080
name: Sequence
namespace: topic
def: Resources for molecular sequences and related data such as alignments and motifs.
alt_id: EDAM:0002228
alt_id: EDAM:0000584
xref: BioCatalogue:Sequence Analysis
is_a: EDAM:0000003 ! Topic
relationship: concerns EDAM:0002403 ! Sequence analysis
relationship: concerns EDAM:0002503 ! Sequence data processing
relationship: concerns EDAM:0000323 ! Phylogenetic tree construction
relationship: is_source_of EDAM:0000849 ! Sequence record
relationship: is_source_of EDAM:0002044 ! Sequence

[Term]
id: EDAM:0000081
name: Structure
namespace: topic
def: Resources for molecular secondary or tertiary (3D) structures and related data such as alignments and structural motifs.
alt_id: EDAM:0002827
alt_id: EDAM:0000585
synonym: "Structure analysis" EXACT []
is_a: EDAM:0000003 ! Topic
relationship: concerns EDAM:0002504 ! Structural data processing
relationship: concerns EDAM:0002484 ! Structure processing

[Term]
id: EDAM:0000084
name: Phylogenetics
namespace: topic
def: Resources for studying evolutionary relationships amongst organisms.
comment: Phylogenetics involves phylogenetic tree construction, typically from molecular sequence or morphological data.  It can be used to analyse the genetic basis of heredity and variation, gene transfer, mode of selection / evolution etc.
xref: BioCatalogue:Phylogeny
xref: BioCatalogue:Statistical Robustness
is_a: EDAM:0000003 ! Topic
relationship: concerns EDAM:0000289 ! Sequence distance matrix generation
relationship: concerns EDAM:0002443 ! Phylogenetic tree processing
relationship: concerns EDAM:0000499 ! Multiple sequence alignment (phylogenetic tree-based)
relationship: concerns EDAM:0000550 ! Phylogenetic model selection
relationship: is_source_of EDAM:0000872 ! Phylogenetic tree

[Term]
id: EDAM:0000088
name: Literature and documentation
namespace: topic
def: Resources concerning the bionformatics literature, bibliographic data and documentation.
xref: BioCatalogue: Document Discovery
xref: BioCatalogue: Literature retrieval
is_a: EDAM:0000003 ! Topic
relationship: concerns EDAM:0000515 ! Tool annotation retrieval
relationship: concerns EDAM:0000516 ! Database annotation retrieval
relationship: concerns EDAM:0002222 ! Ontology annotation retrieval
relationship: concerns EDAM:0002246 ! Demonstration

[Term]
id: EDAM:0000091
name: Data handling
namespace: topic
def: Resources for the generic management of biological data including basic handling of files and databases, datatypes and workflows.
synonym: "Data types, processing and visualisation" EXACT []
is_a: EDAM:0000003 ! Topic
relationship: concerns EDAM:0001780 ! Sequence submission

[Term]
id: EDAM:0000102
name: Sequencing and mapping
namespace: topic
def: Resources concerning the determination and mapping of complete nucleotide sequences.
is_a: EDAM:0000003 ! Topic
relationship: concerns EDAM:0000265 ! Frameshift error detection
relationship: concerns EDAM:0000517 ! PCR primer design (for large scale sequencing)

[Term]
id: EDAM:0000121
name: Proteomics
namespace: topic
def: Resources concerning experimental methods for studying the whole proteomes of organisms.
comment: Proteomics uses high-throughput methods to separate, characterize and identify expressed proteins or analyse protein expression data (for example in different cells or tissues).
alt_id: EDAM:0000764
synonym: "Protein expression" EXACT []
xref: BioCatalogue:Proteomics
is_a: EDAM:0000003 ! Topic

[Term]
id: EDAM:0000200
name: Microarrays
namespace: topic
def: Resources concerning microarrays, for example, to process microarray data or design probes and experiments.
xref: BioCatalogue:Microarrays
is_a: EDAM:0000003 ! Topic
relationship: concerns EDAM:0002432 ! Microarray data processing
relationship: concerns EDAM:0000309 ! Microarray probe design

[Term]
id: EDAM:0000230
name: Sequence generation
namespace: operation
def: Generate a molecular sequence by some means.
is_a: EDAM:0002121 ! Sequence report processing
relationship: has_output EDAM:0002044 ! Sequence

[Term]
id: EDAM:0000231
name: Sequence editing
namespace: operation
def: Edit or change a molecular sequence, either randomly or specifically.
is_a: EDAM:0002121 ! Sequence report processing
relationship: has_output EDAM:0002044 ! Sequence

[Term]
id: EDAM:0000232
name: Sequence merging
namespace: operation
def: Merge two or more (typically overlapping) molecular sequences.
synonym: "Sequence splicing" EXACT []
is_a: EDAM:0002121 ! Sequence report processing
relationship: has_output EDAM:0002044 ! Sequence

[Term]
id: EDAM:0000233
name: Sequence conversion
namespace: operation
def: Convert a molecular sequence from one type to another.
is_a: EDAM:0002121 ! Sequence report processing
relationship: has_output EDAM:0002044 ! Sequence

[Term]
id: EDAM:0000335
name: Report reformatting
namespace: operation
def: Reformat a file of data.
is_a: EDAM:0002409 ! Report processing

[Term]
id: EDAM:0000561
name: Sequence reformatting
namespace: operation
def: Reformat a molecular sequence.
is_a: EDAM:0000335 ! Report reformatting
is_a: EDAM:0002121 ! Sequence report processing
relationship: has_input EDAM:0000849 ! Sequence record
relationship: has_output EDAM:0000849 ! Sequence record

[Term]
id: EDAM:0000562
name: Sequence alignment reformatting
namespace: operation
def: Reformat a molecular sequence alignment.
is_a: EDAM:0000335 ! Report reformatting
is_a: EDAM:0002122 ! Sequence alignment report processing
relationship: has_input EDAM:0000863 ! Sequence alignment
relationship: has_output EDAM:0000863 ! Sequence alignment

[Term]
id: EDAM:0000563
name: Codon usage table reformating
namespace: operation
def: Reformat a codon usage table.
is_a: EDAM:0000335 ! Report reformatting
is_a: EDAM:0002433 ! Codon usage table processing
relationship: has_input EDAM:0001597 ! Codon usage table
relationship: has_output EDAM:0001597 ! Codon usage table

[Term]
id: EDAM:0000586
name: Proteins
namespace: topic
def: Resources concerning proteins.
alt_id: EDAM:0002225
is_a: EDAM:0000003 ! Topic
relationship: concerns EDAM:0002502 ! Protein data processing
relationship: is_source_of EDAM:0000896 ! Protein annotation

[Term]
id: EDAM:0000602
name: Pathways, networks and models
namespace: topic
def: Biological pathways, networks and other models, including the holistic analysis and modelling of biological systems (systems biology).
alt_id: EDAM:0002259
synonym: "Systems biology" EXACT []
xref: BioCatalogue:Pathways
xref: BioCatalogue:Pathway Retrieval
xref: BioCatalogue:Systems Biology
is_a: EDAM:0000003 ! Topic
relationship: concerns EDAM:0002438 ! Pathway or network processing

[Term]
id: EDAM:0000607
name: Laboratory resources
namespace: topic
def: Biological resources for use in the lab including cell lines, viruses, plasmids, phages, DNA probes and primers and so on.
is_a: EDAM:0000003 ! Topic

[Term]
id: EDAM:0000621
name: Organism
namespace: topic
def: Resources concerning a specific organism (e.g. a model organism) or group of organisms, either describing the organism(s) itself or data associated with it.
is_a: EDAM:0000003 ! Topic

[Term]
id: EDAM:0000622
name: Genomics
namespace: topic
def: Resources for the study of whole genomes of one or more organisms, or genomes in general, such as meta-information on genomes, genome projects, gene names etc.
alt_id: EDAM:0000093
alt_id: EDAM:0000794
xref: BioCatalogue:Genomics
xref: BioCatalogue:Functional Genomics
is_a: EDAM:0000003 ! Topic

[Term]
id: EDAM:0000625
name: Genotype and phenotype
namespace: topic
def: Resources concerning genotypes and / or phenotypes especially concerning variations (mutation) and disease.
is_a: EDAM:0000003 ! Topic
relationship: concerns EDAM:0002473 ! Genotype and phenotype annotation retrieval

[Term]
id: EDAM:0000842
name: Identifier
namespace: identifier
def: Something that identifies (typically uniquely) something such as an entity, database, ontology, datatype.
comment: This term is used for datatypes with the sole purpose of identification. It is not used for datatypes which contain other fields not related to identification. See OBO file for regular expression.
relationship: is_identifier_of EDAM:0000006 ! Data

[Term]
id: EDAM:0000850
name: Sequence set
namespace: data
def: A collection of multiple molecular sequences and associated metadata that do not (typically) correspond to molecular sequence database records or entries.
comment: This term may be used for arbitrary sequence sets and associated data arising from processing.
is_a: EDAM:0002806 ! Core data

[Term]
id: EDAM:0000912
name: Nucleic acid physicochemical property
namespace: data
def: A report on the physicochemical properties of a nucleic acid sequence or structure.
comment: This is a broad data type and is used a placeholder for other, more specific types.
is_a: EDAM:0002525 ! Nucleic acid data
is_a: EDAM:0002087 ! Physicochemical property

[Term]
id: EDAM:0001233
name: Sequence set (protein)
namespace: data
def: Any collection of multiple protein sequences and associated metadata that do not (typically) correspond to common sequence database records or database entries.
is_a: EDAM:0000850 ! Sequence set
is_a: EDAM:0002524 ! Protein data

[Term]
id: EDAM:0001234
name: Sequence set (nucleic acid)
namespace: data
def: Any collection of multiple nucleotide sequences and associated metadata that do not (typically) correspond to common sequence database records or database entries.
is_a: EDAM:0000850 ! Sequence set
is_a: EDAM:0002525 ! Nucleic acid data

[Term]
id: EDAM:0001235
name: Sequence cluster
namespace: data
def: A set of sequences that have been clustered or otherwise classified as belonging to a group including (typically) sequence cluster information.
comment: The cluster might include sequences identifiers, short descriptions, alignment and summary information.
is_a: EDAM:0000850 ! Sequence set

[Term]
id: EDAM:0001239
name: Restriction digest
namespace: data
def: Restriction digest fragments from digesting a ucleotide sequence with restriction sites using a restriction endonuclease.
xref: SO:0000412
is_a: EDAM:0001234 ! Sequence set (nucleic acid)

[Term]
id: EDAM:0001246
name: Sequence cluster (nucleic acid)
namespace: data
def: A cluster of nucleotide sequences.
comment: The sequences are typically related, for example a family of sequences.
synonym: "Nucleotide sequence cluster" EXACT []
is_a: EDAM:0001234 ! Sequence set (nucleic acid)
is_a: EDAM:0001235 ! Sequence cluster

[Term]
id: EDAM:0001248
name: Sequence feature location format
namespace: format
def: Format for sequence positions (feature location) as used in DDBJ/EMBL/GenBank database.
comment: See OBO file for URL of format specification.
synonym: "Feature location" EXACT []
is_a: EDAM:0002078 ! Sequence range format
is_a: EDAM:0002330 ! Text format

[Term]
id: EDAM:0001265
name: Sequence composition (base frequencies)
namespace: data
def: A table of base frequencies of a nucleotide sequence.
is_a: EDAM:0001261 ! Sequence composition
is_a: EDAM:0002525 ! Nucleic acid data

[Term]
id: EDAM:0001273
name: Sequence feature table (nucleic acid)
namespace: data
def: Nucleotide sequence feature annotation in any known sequence feature table format.
is_a: EDAM:0001270 ! Sequence feature table
is_a: EDAM:0002525 ! Nucleic acid data

[Term]
id: EDAM:0001276
name: Nucleic acid features
namespace: data
def: Nucleotide sequence-specific feature annotation.
is_a: EDAM:0002525 ! Nucleic acid data
is_a: EDAM:0001255 ! Sequence features

[Term]
id: EDAM:0001295
name: quicktandem
namespace: format
def: Report format for tandem repeats in a nucleotide sequence (format generated by the Sanger Centre quicktandem program).
comment: See OBO file for URL of format specification.
is_a: EDAM:0002155 ! Sequence features (repeats) format
is_a: EDAM:0002330 ! Text format

[Term]
id: EDAM:0001296
name: Sanger inverted repeat sequence report format
namespace: format
def: Report format for inverted repeats in a nucleotide sequence (format generated by the Sanger Centre inverted program).
comment: See OBO file for URL of format specification.
is_a: EDAM:0002155 ! Sequence features (repeats) format
is_a: EDAM:0002330 ! Text format

[Term]
id: EDAM:0001297
name: EMBOSS repeat sequence report format
namespace: format
def: Report format for tandem repeats in a sequence (an EMBOSS report format).
comment: See OBO file for URL of format specification.
is_a: EDAM:0002155 ! Sequence features (repeats) format
is_a: EDAM:0002330 ! Text format

[Term]
id: EDAM:0001316
name: est2genome
namespace: format
def: Format of a report on exon-intron structure generated by EMBOSS est2genome.
comment: See OBO file for URL of format specification.
is_a: EDAM:0002159 ! Gene annotation (coding region) format
is_a: EDAM:0002330 ! Text format

[Term]
id: EDAM:0001318
name: restrict
namespace: format
def: Report format for restriction enzyme recognition sites used by EMBOSS restrict program.
comment: See OBO file for URL of format specification.
is_a: EDAM:0002158 ! Nucleic acid features (restriction sites) format
is_a: EDAM:0002330 ! Text format

[Term]
id: EDAM:0001319
name: restover
namespace: format
def: Report format for restriction enzyme recognition sites used by EMBOSS restover program.
comment: See OBO file for URL of format specification.
is_a: EDAM:0002158 ! Nucleic acid features (restriction sites) format
is_a: EDAM:0002330 ! Text format

[Term]
id: EDAM:0001320
name: REBASE restriction site report format
namespace: format
def: Report format for restriction enzyme recognition sites used by REBASE database.
comment: See OBO file for URL of format specification.
is_a: EDAM:0002158 ! Nucleic acid features (restriction sites) format
is_a: EDAM:0002330 ! Text format

[Term]
id: EDAM:0001334
name: mspcrunch
namespace: format
def: Format of results of a sequence database search using some variant of MSPCrunch.
comment: See OBO file for URL of format specification.
is_a: EDAM:0002066 ! Database hits (sequence) format
is_a: EDAM:0002330 ! Text format

[Term]
id: EDAM:0001335
name: smith-waterman
namespace: format
def: Format of results of a sequence database search using some variant of Smith Waterman.
comment: See OBO file for URL of format specification.
is_a: EDAM:0002066 ! Database hits (sequence) format
is_a: EDAM:0002330 ! Text format

[Term]
id: EDAM:0001336
name: dhf
namespace: format
def: Format of EMBASSY domain hits file (DHF) of hits (sequences) with domain classification information.
comment: The hits are relatives to a SCOP or CATH family and are found from a search of a sequence database. See OBO file for URL of format specification.
is_a: EDAM:0002066 ! Database hits (sequence) format
is_a: EDAM:0002330 ! Text format

[Term]
id: EDAM:0001337
name: lhf
namespace: format
def: Format of EMBASSY ligand hits file (LHF) of database hits (sequences) with ligand classification information.
comment: The hits are putative ligand-binding sequences and are found from a search of a sequence database. See OBO file for URL of format specification.
is_a: EDAM:0002066 ! Database hits (sequence) format
is_a: EDAM:0002330 ! Text format

[Term]
id: EDAM:0001349
name: HMMER Dirichlet prior record
namespace: format
def: Dirichlet distribution HMMER format.
comment: See OBO file for URL of format specification.
is_a: EDAM:0002074 ! Dirichlet distribution format
is_a: EDAM:0002330 ! Text format

[Term]
id: EDAM:0001350
name: MEME Dirichlet prior record
namespace: format
def: Dirichlet distribution MEME format.
comment: See OBO file for URL of format specification.
is_a: EDAM:0002074 ! Dirichlet distribution format
is_a: EDAM:0002330 ! Text format

[Term]
id: EDAM:0001351
name: HMMER emission and transition count report
namespace: format
def: Format of a report from the HMMER package on the emission and transition counts of a hidden Markov model.
comment: See OBO file for URL of format specification.
is_a: EDAM:0002075 ! HMM emission and transition counts format
is_a: EDAM:0002330 ! Text format

[Term]
id: EDAM:0001356
name: prosite-pattern
namespace: format
def: Format of a regular expression pattern from the Prosite database.
comment: See OBO file for URL of format specification.
is_a: EDAM:0002068 ! Sequence motif format
is_a: EDAM:0002330 ! Text format

[Term]
id: EDAM:0001357
name: EMBOSS sequence pattern
namespace: format
def: Format of an EMBOSS sequence pattern.
comment: See OBO file for URL of format specification.
is_a: EDAM:0002068 ! Sequence motif format
is_a: EDAM:0002330 ! Text format

[Term]
id: EDAM:0001360
name: meme-motif
namespace: format
def: A motif in the format generated by the MEME program.
comment: See OBO file for URL of format specification.
is_a: EDAM:0002068 ! Sequence motif format
is_a: EDAM:0002330 ! Text format

[Term]
id: EDAM:0001366
name: prosite-profile
namespace: format
def: Sequence profile (sequence classifier) format used in the PROSITE database.
comment: See OBO file for URL of format specification.
is_a: EDAM:0002069 ! Sequence profile format
is_a: EDAM:0002330 ! Text format

[Term]
id: EDAM:0001367
name: jaspar
namespace: format
def: A profile (sequence classifier) in the format used in the JASPAR database.
comment: See OBO file for URL of format specification.
is_a: EDAM:0002069 ! Sequence profile format
is_a: EDAM:0002330 ! Text format

[Term]
id: EDAM:0001369
name: MEME background Markov model format
namespace: format
def: Format of the model of random sequences used by MEME.
comment: See OBO file for URL of format specification.
is_a: EDAM:0002072 ! Hidden Markov model format
is_a: EDAM:0002330 ! Text format

[Term]
id: EDAM:0001370
name: HMMER hidden Markov model format
namespace: format
def: Format of a hidden Markov model representation used by the HMMER package.
comment: See OBO file for URL of format specification.
is_a: EDAM:0002072 ! Hidden Markov model format
is_a: EDAM:0002330 ! Text format

[Term]
id: EDAM:0001383
name: Sequence alignment (nucleic acid)
namespace: data
def: Alignment of multiple nucleotide sequences.
is_a: EDAM:0000863 ! Sequence alignment
is_a: EDAM:0002525 ! Nucleic acid data

[Term]
id: EDAM:0001419
name: Sequence-MEME profile alignment format
namespace: format
def: Format for alignment of molecular sequences to MEME profiles (position-dependent scoring matrices) as generated by the MAST tool from the MEME package.
comment: See OBO file for URL of format specification.
is_a: EDAM:0002014 ! Sequence-profile alignment format
is_a: EDAM:0002330 ! Text format

[Term]
id: EDAM:0001421
name: HMMER alignment report format (sequences versus HMMs)
namespace: format
def: Format used by the HMMER package for an alignment of a sequence against a hidden Markov model database.
comment: See OBO file for URL of format specification.
is_a: EDAM:0002014 ! Sequence-profile alignment format
is_a: EDAM:0002330 ! Text format

[Term]
id: EDAM:0001422
name: HMMER alignment report format (HMM versus sequences)
namespace: format
def: Format used by the HMMER package for of an alignment of a hidden Markov model against a sequence database.
comment: See OBO file for URL of format specification.
is_a: EDAM:0002014 ! Sequence-profile alignment format
is_a: EDAM:0002330 ! Text format

[Term]
id: EDAM:0001423
name: PHYLIP phylogenetic distance matrix format
namespace: format
def: Format of PHYLIP phylogenetic distance matrix data.
comment: Data Type must include the distance matrix, probably as pairs of sequence identifiers with a distance (integer or float). See OBO file for URL of format specification.
is_a: EDAM:0002067 ! Sequence distance matrix format
is_a: EDAM:0002330 ! Text format

[Term]
id: EDAM:0001430
name: PHYLIP continuous quantitative characters format
namespace: format
def: PHYLIP file format for continuous quantitative character data.
comment: See OBO file for URL of format specification.
is_a: EDAM:0002037 ! Phylogenetic continuous quantitative character format
is_a: EDAM:0002330 ! Text format

[Term]
id: EDAM:0001432
name: PHYLIP phylogenetic character frequencies
namespace: format
def: PHYLIP file format for phylogenetics character frequency data.
comment: See OBO file for URL of format specification.
is_a: EDAM:0002037 ! Phylogenetic continuous quantitative character format
is_a: EDAM:0002330 ! Text format

[Term]
id: EDAM:0001433
name: PHYLIP discrete states format
namespace: format
def: Format of PHYLIP discrete states data.
comment: See OBO file for URL of format specification.
is_a: EDAM:0002038 ! Phylogenetic discrete states format
is_a: EDAM:0002330 ! Text format

[Term]
id: EDAM:0001434
name: PHYLIP cliques file format
namespace: format
def: Format of PHYLIP cliques data.
comment: See OBO file for URL of format specification.
is_a: EDAM:0002039 ! Phylogenetic metadata (cliques) format
is_a: EDAM:0002330 ! Text format

[Term]
id: EDAM:0001445
name: Phylip phylogenetic tree distance data format
namespace: format
def: Format for distances, such as Branch Score distance, between two or more phylogenetic trees as used by the Phylip package.
comment: See OBO file for URL of format specification.
is_a: EDAM:0002049 ! Phylogenetic metadata (tree distances) format
is_a: EDAM:0002330 ! Text format

[Term]
id: EDAM:0001454
name: dssp
namespace: format
def: Format of an entry from the DSSP database (Dictionary of Secondary Structure in Proteins).
comment: The DSSP database is built using the DSSP application which defines secondary structure, geometrical features and solvent exposure of proteins, given atomic coordinates in PDB format. See OBO file for URL of format specification.
is_a: EDAM:0002077 ! Protein secondary structure format
is_a: EDAM:0002330 ! Text format

[Term]
id: EDAM:0001455
name: hssp
namespace: format
def: Entry format of the HSSP database (Homology-derived Secondary Structure in Proteins).
comment: See OBO file for URL of format specification.
is_a: EDAM:0002077 ! Protein secondary structure format
is_a: EDAM:0002330 ! Text format

[Term]
id: EDAM:0001457
name: Vienna RNA secondary structure format
namespace: format
def: Format of RNA secondary structure (in bracket notation) with free energy values, generated by the Vienna program.
comment: See OBO file for URL of format specification.
is_a: EDAM:0002076 ! RNA secondary structure format
is_a: EDAM:0002330 ! Text format

[Term]
id: EDAM:0001458
name: Vienna local RNA secondary structure format
namespace: format
def: Format of local RNA secondary structure components with free energy values, generated by the Vienna program.
comment: See OBO file for URL of format specification.
is_a: EDAM:0002076 ! RNA secondary structure format
is_a: EDAM:0002330 ! Text format

[Term]
id: EDAM:0001459
name: Nucleic acid structure
namespace: data
def: 3D coordinate and associated data for a nucleic acid tertiary (3D) structure.
is_a: EDAM:0000883 ! Structure
is_a: EDAM:0002525 ! Nucleic acid data

[Term]
id: EDAM:0001476
name: PDB format
namespace: format
def: Entry format of PDB database in PDB format, or any report in the same format.
comment: See OBO file for URL of format specification.
synonym: "PDB" EXACT []
xref: Moby:PDB-formatted-text
xref: Moby:PDB-Text
is_a: EDAM:0001475 ! PDB database entry format
is_a: EDAM:0002330 ! Text format

[Term]
id: EDAM:0001477
name: mmCIF
namespace: format
def: Entry format of PDB database in mmCIF format, or any report in the same format.
comment: See OBO file for URL of format specification.
synonym: "mmcif" EXACT []
xref: Moby:mmCIF-Text
xref: Moby:mmCIF_Text
is_a: EDAM:0001475 ! PDB database entry format
is_a: EDAM:0002330 ! Text format

[Term]
id: EDAM:0001482
name: Tertiary structure alignment (nucleic acid)
namespace: data
def: Alignment (superimposition) of nucleic acid tertiary (3D) structures.
is_a: EDAM:0000886 ! Tertiary structure alignment
is_a: EDAM:0002525 ! Nucleic acid data

[Term]
id: EDAM:0001500
name: Domainatrix 3D-1D scoring matrix format
namespace: format
def: Format of a matrix of 3D-1D scores used by the EMBOSS Domainatrix applications.
comment: See OBO file for URL of format specification.
is_a: EDAM:0002064 ! 3D-1D scoring matrix format
is_a: EDAM:0002330 ! Text format

[Term]
id: EDAM:0001504
name: aaindex
namespace: format
def: Amino acid index format used by the AAindex database.
comment: See OBO file for URL of format specification.
is_a: EDAM:0002017 ! Amino acid index format
is_a: EDAM:0002330 ! Text format

[Term]
id: EDAM:0001551
name: Pcons report format
namespace: format
def: Format of output of the Pcons Model Quality Assessment Program (MQAP).
comment: Pcons ranks protein models by assessing their quality based on the occurrence of recurring common three-dimensional structural patterns. Pcons returns a score reflecting the overall global quality and a score for each individual residue in the protein reflecting the local residue quality. See OBO file for URL of format specification.
is_a: EDAM:0002065 ! Protein structure annotation (quality evaluation) format
is_a: EDAM:0002330 ! Text format

[Term]
id: EDAM:0001552
name: ProQ report format
namespace: format
def: Format of output of the ProQ protein model quality predictor.
comment: ProQ is a neural network-based predictor that predicts the quality of a protein model based on the number of structural features. See OBO file for URL of format specification.
is_a: EDAM:0002065 ! Protein structure annotation (quality evaluation) format
is_a: EDAM:0002330 ! Text format

[Term]
id: EDAM:0001582
name: findkm
namespace: format
def: A report format for the kinetics of enzyme-catalysed reaction(s) in a format generated by EMBOSS findkm. This includes Michaelis Menten plot, Hanes Woolf plot, Michaelis Menten constant (Km) and maximum velocity (Vmax).
comment: See OBO file for URL of format specification.
is_a: EDAM:0002027 ! Enzyme kinetics report format
is_a: EDAM:0002330 ! Text format

[Term]
id: EDAM:0001627
name: Primer3 primer report format
namespace: format
def: Report format on PCR primers and hybridization oligos as generated by Whitehead primer3 program.
comment: See OBO file for URL of format specification.
is_a: EDAM:0002061 ! Nucleic acid features (primers) format
is_a: EDAM:0002330 ! Text format

[Term]
id: EDAM:0001629
name: mira
namespace: format
def: Format of MIRA sequence trace information file.
comment: See OBO file for URL of format specification.
is_a: EDAM:0002057 ! Sequence trace format
is_a: EDAM:0002330 ! Text format

[Term]
id: EDAM:0001630
name: CAF
namespace: format
def: Common Assembly Format (CAF). A sequence assembly format including contigs, base-call qualities, and other metadata.
spec_url: http://www.sanger.ac.uk/resources/software/caf/
is_a: EDAM:0002330 ! Text format
is_a: EDAM:0002561 ! Sequence assembly format (text)
relationship: is_format_of EDAM:0000925 ! Sequence assembly

[Term]
id: EDAM:0001633
name: PHD
namespace: format
def: PHD sequence trace format to store serialised chromatogram data (reads).
spec_url: http://www.bioperl.org/wiki/PHD_sequence_format
is_a: EDAM:0002330 ! Text format
relationship: is_format_of EDAM:0000924 ! Sequence trace

[Term]
id: EDAM:0001637
name: dat
namespace: format
def: Format of Affymetrix data file of raw image data.
comment: See OBO file for URL of format specification.
synonym: "Affymetrix image data file format" EXACT []
is_a: EDAM:0002058 ! Gene annotation (expression) format
is_a: EDAM:0002330 ! Text format

[Term]
id: EDAM:0001638
name: cel
namespace: format
def: Format of Affymetrix data file of information about (raw) expression levels of the individual probes.
comment: See OBO file for URL of format specification.
synonym: "Affymetrix probe raw data format" EXACT []
is_a: EDAM:0002058 ! Gene annotation (expression) format
is_a: EDAM:0002330 ! Text format

[Term]
id: EDAM:0001639
name: affymetrix
namespace: format
def: Format of affymetrix gene cluster files (hc-genes.txt, hc-chips.txt) from hierarchical clustering.
comment: See OBO file for URL of format specification.
is_a: EDAM:0002330 ! Text format

[Term]
id: EDAM:0001641
name: affymetrix-exp
namespace: format
def: Affymetrix data file format for information about experimental conditions and protocols.
comment: See OBO file for URL of format specification.
synonym: "Affymetrix experimental conditions data file format" EXACT []
is_a: EDAM:0002056 ! Microarray experiment data format
is_a: EDAM:0002330 ! Text format

[Term]
id: EDAM:0001644
name: chp
namespace: format
def: Format of Affymetrix data file of information about (normalised) expression levels of the individual probes.
comment: See OBO file for URL of format specification.
synonym: "Affymetrix probe normalised data format" EXACT []
is_a: EDAM:0002058 ! Gene annotation (expression) format
is_a: EDAM:0002330 ! Text format

[Term]
id: EDAM:0001705
name: HET group dictionary entry format
namespace: format
def: The format of an entry from the HET group dictionary (HET groups from PDB files).
comment: See OBO file for URL of format specification.
is_a: EDAM:0002030 ! Small molecule annotation format
is_a: EDAM:0002330 ! Text format

[Term]
id: EDAM:0001739
name: pmc
namespace: format
def: Article format of the PubMed Central database.
comment: See OBO file for URL of format specification.
is_a: EDAM:0002020 ! Article format
is_a: EDAM:0002330 ! Text format

[Term]
id: EDAM:0001740
name: iHOP text mining abstract format
namespace: format
def: iHOP abstract format.
comment: See OBO file for URL of format specification.
is_a: EDAM:0002021 ! Text mining report format
is_a: EDAM:0002330 ! Text format

[Term]
id: EDAM:0001741
name: Oscar3 text mining abstract format
namespace: format
def: Text mining abstract format from the Oscar 3 application.
comment: Oscar 3 performs chemistry-specific parsing of chemical documents. It attempts to identify chemical names, ontology terms and chemical data from a document. See OBO file for URL of format specification.
is_a: EDAM:0002021 ! Text mining report format
is_a: EDAM:0002330 ! Text format

[Term]
id: EDAM:0001747
name: PDB atom record format
namespace: format
def: Format of an ATOM record (describing data for an individual atom) from a PDB file.
comment: See OBO file for URL of format specification.
is_a: EDAM:0001918 ! Atomic data format
is_a: EDAM:0002330 ! Text format

[Term]
id: EDAM:0001848
name: Tertiary structure reformatting
namespace: operation
def: Reformat a file of tertiary structure data.
xref: WHATIF: PDBasXML
is_a: EDAM:0000335 ! Report reformatting
is_a: EDAM:0002234 ! Tertiary structure report processing

[Term]
id: EDAM:0001861
name: PlasMapper TextMap plasmid map format
namespace: format
def: Map of a plasmid (circular DNA) in PlasMapper TextMap format.
comment: See OBO file for URL of format specification.
xref: Moby:PlasMapperTextMap
is_a: EDAM:0002060 ! Map format
is_a: EDAM:0002330 ! Text format

[Term]
id: EDAM:0001915
name: Format
namespace: format
def: An exchange format of particular type of data.
comment: Common formats used by multiple independent tools and main formats used by public databases are listed.

[Term]
id: EDAM:0001961
name: stockholm
namespace: format
def: Stockholm multiple sequence alignment format (used by Pfam and Rfam).
spec_url: http://en.wikipedia.org/wiki/Stockholm_format
is_a: EDAM:0002330 ! Text format
relationship: is_format_of EDAM:0000863 ! Sequence alignment

[Term]
id: EDAM:0001974
name: GFF
namespace: format
def: General Feature Format (GFF) of sequence features.
comment: Current version is 2 (GFF2). GFF3 is a slightly different, richer format and uses ontology terms. See OBO file for URL of format specification.
synonym: "GFF2" EXACT []
spec_url: http://www.sanger.ac.uk/resources/software/gff/spec.html
is_a: EDAM:0002330 ! Text format
relationship: is_format_of EDAM:0001255 ! Sequence features

[Term]
id: EDAM:0001975
name: GFF3
namespace: format
def: Generic Feature Format version 3 (GFF3) of sequence features.
comment: As opposed to GFF (GFF2), GFF3 is a slightly different, richer format and uses ontology terms. See OBO file for URL of format specification.
spec_url: http://sequenceontology.org/resources/gff3.html
is_a: EDAM:0002330 ! Text format
relationship: is_format_of EDAM:0001255 ! Sequence features

[Term]
id: EDAM:0001979
name: debug-feat
namespace: format
def: EMBOSS debugging trace feature format of full internal data content.
comment: See OBO file for URL of format specification.
is_a: EDAM:0001920 ! Sequence feature annotation format
is_a: EDAM:0002330 ! Text format

[Term]
id: EDAM:0002035
name: Chemical formula format
namespace: format
def: Text format of a chemical formula.
comment: See OBO file for URL of format specification.
is_a: EDAM:0002350 ! Datatype format
is_a: EDAM:0002330 ! Text format

[Term]
id: EDAM:0002070
name: Sequence motif (nucleic acid)
namespace: data
def: A nucleotide sequence motif.
is_a: EDAM:0001353 ! Sequence motif
is_a: EDAM:0002525 ! Nucleic acid data

[Term]
id: EDAM:0002084
name: Nucleic acid annotation
namespace: data
def: An informative report about a specific nucleic acid.
is_a: EDAM:0002529 ! Molecular annotation
is_a: EDAM:0002525 ! Nucleic acid data

[Term]
id: EDAM:0002121
name: Sequence report processing
namespace: operation
def: Perform basic (non-analytical) operations on (a report or file of( sequences (which might include features), such as file creation or concatenation, removal or ordering of sequences.
is_a: EDAM:0002446 ! Sequence processing
is_a: EDAM:0002409 ! Report processing

[Term]
id: EDAM:0002181
name: EMBL-like format (text)
namespace: format
def: A text format resembling EMBL entry format.
comment: This term may be used for the many non-standard EMBL-like text formats. See OBO file for URL of format specification.
is_a: EDAM:0002543 ! EMBL-like
is_a: EDAM:0002330 ! Text format

[Term]
id: EDAM:0002182
name: FASTQ-like format (text)
namespace: format
def: A text format resembling FASTQ short read format.
comment: This term may be used for non-standard FASTQ short read-like formats. See OBO file for URL of format specification.
is_a: EDAM:0002545 ! FASTQ-like
is_a: EDAM:0002330 ! Text format

[Term]
id: EDAM:0002187
name: uniprotkb-like format (text)
namespace: format
def: A text sequence format resembling uniprotkb entry format.
comment: See OBO file for URL of format specification.
is_a: EDAM:0002547 ! uniprotkb-like
is_a: EDAM:0002330 ! Text format

[Term]
id: EDAM:0002194
name: medline
namespace: format
def: Abstract format used by MedLine database.
comment: See OBO file for URL of format specification.
is_a: EDAM:0002020 ! Article format
is_a: EDAM:0002330 ! Text format

[Term]
id: EDAM:0002197
name: OWL
namespace: format
def: OWL ontology format.
comment: See OBO file for URL of format specification.
is_a: EDAM:0002195 ! Ontology format
is_a: EDAM:0002330 ! Text format

[Term]
id: EDAM:0002198
name: Gene cluster
namespace: data
def: A cluster of similar genes.
is_a: EDAM:0001246 ! Sequence cluster (nucleic acid)

[Term]
id: EDAM:0002200
name: FASTA-like format (text)
namespace: format
def: A text format resembling FASTA format.
comment: This term may be used for the many non-standard FASTA-like formats. See OBO file for URL of format specification.
is_a: EDAM:0002546 ! FASTA-like
is_a: EDAM:0002330 ! Text format

[Term]
id: EDAM:0002205
name: GenBank-like format (text)
namespace: format
def: A text format resembling GenBank entry (plain text) format.
comment: This term may be used for the non-standard GenBank-like text formats. See OBO file for URL of format specification.
is_a: EDAM:0002559 ! GenBank-like
is_a: EDAM:0002330 ! Text format

[Term]
id: EDAM:0002206
name: Sequence feature table format (text)
namespace: format
def: Text format for a sequence feature table.
comment: See OBO file for URL of format specification.
is_a: EDAM:0002548 ! Sequence feature table format
is_a: EDAM:0002330 ! Text format

[Term]
id: EDAM:0002230
name: Classification
namespace: topic
def: Resources that help to identify, group, or name things in a structured way according to some schema based on observable relationships.
is_a: EDAM:0000003 ! Topic

[Term]
id: EDAM:0002245
name: Sequence set (bootstrapped)
namespace: data
def: A collection of sequences output from a bootstrapping (resampling) procedure.
comment: Bootstrapping is often performed in phylogenetic analysis.
is_a: EDAM:0000850 ! Sequence set

[Term]
id: EDAM:0002330
name: Text format
namespace: format
def: Text format.
comment: Data in text format can be compressed into binary format, or can be a value of an XML element or attribute.
is_a: EDAM:0001915 ! Format

[Term]
id: EDAM:0002334
name: URI format
namespace: format
def: Typical textual representation of a URI.
comment: See OBO file for URL of format specification.
is_a: EDAM:0002330 ! Text format
is_a: EDAM:0002350 ! Datatype format

[Term]
id: EDAM:0002354
name: RNA family annotation
namespace: data
def: An informative report on a specific RNA family or other group of classified RNA sequences.
is_a: EDAM:0002018 ! Metadata and annotation
is_a: EDAM:0002525 ! Nucleic acid data

[Term]
id: EDAM:0002525
name: Nucleic acid data
namespace: data
def: Data concerning one or more nucleic acid molecules.
is_a: EDAM:0002528 ! Molecular data

[Term]
id: EDAM:0002549
name: OBO
namespace: format
def: OBO ontology text format.
comment: See OBO file for URL of format specification.
is_a: EDAM:0002196 ! OBO format
is_a: EDAM:0002330 ! Text format

[Term]
id: EDAM:0002551
name: Sequence record format (text)
namespace: format
def: Data format for a molecular sequence record.
comment: See OBO file for URL of format specification.
is_a: EDAM:0001919 ! Sequence record format
is_a: EDAM:0002330 ! Text format

[Term]
id: EDAM:0002554
name: Alignment format (text)
namespace: format
def: Text format for molecular sequence alignment information.
comment: See OBO file for URL of format specification.
is_a: EDAM:0001921 ! Alignment format
is_a: EDAM:0002330 ! Text format

[Term]
id: EDAM:0002556
name: Phylogenetic tree format (text)
namespace: format
def: Text format for a phylogenetic tree.
comment: See OBO file for URL of format specification.
is_a: EDAM:0002006 ! Phylogenetic tree format
is_a: EDAM:0002330 ! Text format

[Term]
id: EDAM:0002562
name: Amino acid identifier format
namespace: format
def: Text format (representation) of amino acid residues.
comment: See OBO file for URL of format specification.
is_a: EDAM:0002350 ! Datatype format
is_a: EDAM:0002330 ! Text format

[Term]
id: EDAM:0002573
name: SAM
namespace: format
def: 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.
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. See OBO file for URL of format specification.
spec_url: http://samtools.sourceforge.net/SAM-1.3.pdf
is_a: EDAM:0002057 ! Sequence trace format
is_a: EDAM:0001921 ! Alignment format
is_a: EDAM:0002330 ! Text format
relationship: is_format_of EDAM:0001383 ! Sequence alignment (nucleic acid)
relationship: is_format_of EDAM:0001381 ! Sequence alignment (pair)

[Term]
id: EDAM:0002816
name: Genes
namespace: topic
def: Resources concerning the study of genes.
is_a: EDAM:0000003 ! Topic
is_a: EDAM:0000640 ! Nucleic acid sequences
relationship: concerns EDAM:0002472 ! Gene annotation retrieval

[Term]
id: EDAM:0002829
name: Ontologies and nomenclature
namespace: topic
def: Resources and study on conceptualisation and naming.
is_a: EDAM:0000003 ! Topic

[Term]
id: EDAM:0002841
name: Informatics
namespace: topic
def: A sub-discipline of bioinformatics; the application of information technology to a specialised biological area.
is_a: EDAM:0000003 ! Topic

[Term]
id: EDAM:0002874
name: Sequence set (polymorphic)
namespace: data
def: A set of sub-sequences displaying some type of polymorphism, typically indicating the sequence in which they occur, their position and other metadata.
is_a: EDAM:0001234 ! Sequence set (nucleic acid)

[Term]
id: EDAM:0003001
name: ACE
namespace: format
def: ACE sequence assembly format including contigs, base-call qualities, and other metadata (version Aug 1998 and onwards).
spec_url: http://bozeman.mbt.washington.edu/consed/distributions/README.14.0.txt
is_a: EDAM:0002330 ! Text format
relationship: is_format_of EDAM:0000925 ! Sequence assembly

[Term]
id: EDAM:0003003
name: BED
namespace: format
def: BED format of sequence annotation track, typically to be displayed in a genome browser.
comment: BED detail format includes 2 additional columns (http://genome.ucsc.edu/FAQ/FAQformat#format1.7) and BED 15 includes 3 additional columns for experiment scores (http://genomewiki.ucsc.edu/index.php/Microarray_track).
spec_url: http://genome.ucsc.edu/FAQ/FAQformat#format1
is_a: EDAM:0002330 ! Text format
relationship: is_format_of EDAM:0003002 ! Sequence annotation track

[Term]
id: EDAM:0003005
name: WIG
namespace: format
def: Wiggle format (WIG) of a sequence annotation track that consists of a value for each sequence position. Typically to be displayed in a genome browser.
spec_url: http://genome.ucsc.edu/goldenPath/help/wiggle.html
is_a: EDAM:0002330 ! Text format
relationship: is_format_of EDAM:0003002 ! Sequence annotation track

[Term]
id: EDAM:0003007
name: PSL
namespace: format
def: PSL format of alignments, typically generated by BLAT or psLayout. Can be displayed in a genome browser like a sequence annotation track.
spec_url: http://genome.ucsc.edu/FAQ/FAQformat#format2
is_a: EDAM:0002330 ! Text format
relationship: is_format_of EDAM:0001381 ! Sequence alignment (pair)
relationship: is_format_of EDAM:0003002 ! Sequence annotation track

[Term]
id: EDAM:0003008
name: MAF (Multiple Alignment Format)
namespace: format
def: Multiple Alignment Format (MAF) supporting alignments of whole genomes with rearrangements, directions, multiple pieces to the alignment, and so forth. Typically generated by Multiz and TBA aligners; can be displayed in a genome browser like a sequence annotation track.
spec_url: http://genome.ucsc.edu/FAQ/FAQformat#format5
is_a: EDAM:0002330 ! Text format
relationship: is_format_of EDAM:0000863 ! Sequence alignment
relationship: is_format_of EDAM:0003002 ! Sequence annotation track

[Term]
id: EDAM:0003011
name: genePred
namespace: format
def: genePred table format for gene prediction tracks.
comment: genePred format has 3 main variations (http://genome.ucsc.edu/FAQ/FAQformat#format9 http://www.broadinstitute.org/software/igv/genePred). They reflect UCSC Browser DB tables.
spec_url: http://genome.ucsc.edu/FAQ/FAQformat#format9
is_a: EDAM:0002330 ! Text format
relationship: is_format_of EDAM:0003002 ! Sequence annotation track

[Term]
id: EDAM:0003012
name: pgSnp
namespace: format
def: Personal Genome SNP (pgSnp) format for sequence variation tracks (indels and polymorphisms), supported by the UCSC Genome Browser.
spec_url: http://genome.ucsc.edu/FAQ/FAQformat#format10
is_a: EDAM:0002330 ! Text format
relationship: is_format_of EDAM:0003002 ! Sequence annotation track

[Term]
id: EDAM:0003013
name: axt
namespace: format
def: axt format of alignments, typically produced from BLASTZ.
spec_url: http://genome.ucsc.edu/goldenPath/help/axt.html
is_a: EDAM:0002330 ! Text format
relationship: is_format_of EDAM:0001381 ! Sequence alignment (pair)

[Term]
id: EDAM:0003014
name: LAV
namespace: format
def: LAV format of alignments generated by BLASTZ and LASTZ.
spec_url: http://www.bx.psu.edu/miller_lab/dist/lav_format.html
is_a: EDAM:0002330 ! Text format
relationship: is_format_of EDAM:0001381 ! Sequence alignment (pair)

[Term]
id: EDAM:0003015
name: Pileup
namespace: format
def: Pileup format of alignment of sequences (e.g. sequencing reads) to (a) reference sequence(s). Contains aligned bases per base of the reference sequence(s).
comment: See OBO file for URL of format specification.
spec_url: http://samtools.sourceforge.net/pileup.shtml
is_a: EDAM:0002330 ! Text format
relationship: is_format_of EDAM:0001381 ! Sequence alignment (pair)

[Term]
id: EDAM:0003016
name: VCF
namespace: format
def: Variant Call Format (VCF) for sequence variation (indels, polymorphisms, structural variation).
spec_url: http://vcftools.sourceforge.net/specs.html
is_a: EDAM:0002330 ! Text format
relationship: is_format_of EDAM:0001255 ! Sequence features