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font-size: 15px;"> <i class="fa-brands fa-bluesky" aria-hidden="true"></i> </a> </li> <li> <a href="https://www.facebook.com/pages/Gene-Ontology/305908656519" target="blank" style="padding: 8px 3px; font-size: 15px;"> <i class="fa-brands fa-facebook-f" aria-hidden="true"></i> </a> </li> <li> <a href="https://github.com/geneontology" target="blank" style="padding: 8px 3px; font-size: 15px;"> <i class="fa-brands fa-github" aria-hidden="true"></i> </a> </li> <li style="margin-right: 5px"> <a href="https://genomic.social/@go" target="blank" style="padding: 8px 3px; font-size: 15px;"> <i class="fa-brands fa-mastodon" aria-hidden="true"></i> </a> </li> </ul> <a href="https://www.alliancegenome.org" target="blank" alt="Alliance of Genome Resources" > <img src="/assets/ALLIANCE-logo-nobackground_foundingmember.png" alt="Alliance of Genome Resources" style="height: 60px; margin-right: 10px;"/> </a> </div> </div> </div> </nav> <div class="page-content"> <div class="wrapper"> <div class="container u-padding-bottom-xlarge" style="width: 100%;"> <div class="row"> <article id="markdown-content-container" class="container" style="width:90%"> <h1 id="go-annotation-file-gaf-22">GO Annotation File (GAF) 2.2</h1> <p>This guide lays out the format specifications for the <strong>G</strong>ene <strong>A</strong>ssociation <strong>F</strong>ile (GAF) 2.2 introduced in March 2021; for the older format please see the <a href="/docs/go-annotation-file-gaf-format-2.1/">GAF 2.1 guide</a>.</p> <p>The Gene Ontology Consortium stores annotation data, the representation of gene product attributes using GO terms, in standardized tab-delimited text files. Each line in the file represents a single association between a gene product and a GO term, with an <a href="/docs/guide-go-evidence-codes/">evidence code</a> and the reference to support the link.</p> <p>GO also provides annotations as <a href="/docs/gene-product-association-data-gpad-format/">GPAD</a>+<a href="/docs/gene-product-information-gpi-format/">GPI</a> (companion files). For more general information on annotation, please see the <a href="/docs/go-annotations/">introduction to GO annotation</a>.</p> <h2 id="changes-between-the-go-annotation-file-gaf-format-21-and-22">Changes between the GO Annotation File (GAF) format 2.1 and 2.2</h2> <p><strong>Header</strong></p> <ul> <li><strong>The <code class="highlighter-rouge">gaf-version</code> header must read <code class="highlighter-rouge">2.2</code> for this format.</strong></li> <li><strong>The header must also contain ‘generated-by’ and ‘date-generated’ lines.</strong></li> </ul> <p><strong>Columns</strong></p> <ul> <li><strong>Column 4 (“Relation”) is now required.</strong> <ul> <li><strong>Column 4 (“Relation”) may optionally be negated (“NOT”) by pipe-separating the relation with ‘NOT’, e.g. NOT|enables.</strong></li> <li><strong>Column 4 (“Relation”) was previously named “Qualifier”</strong></li> </ul> </li> </ul> <h2 id="go-annotation-file-gaf-22-1">GO Annotation File (GAF) 2.2</h2> <h3 id="gaf-header">GAF Header</h3> <p>All gene association files must start with a single line denoting the file format, as follows:</p> <div class="highlighter-rouge"><pre class="highlight"><code>!gaf-version: 2.2 </code></pre> </div> <p>Other information, such as contact details for the submitter or database group, useful link, etc., can be included in an association file by prefixing the line with an exclamation mark (!); such lines will be ignored by parsers.</p> <p>Required information to provide in the header:</p> <div class="highlighter-rouge"><pre class="highlight"><code>!generated-by: database listed in dbxrefs.yaml !date-generated: YYYY-MM-DD or YYYY-MM-DDTHH:MM </code></pre> </div> <p>Groups may decide to include additional information. Examples include:</p> <div class="highlighter-rouge"><pre class="highlight"><code>!URL: e.g. http://www.yeastgenome.org/ !Project-release: e.g. WS275 !Funding: e.g. NHGRI !Columns: file format written out !go-version: PURL !ro-version: PURL !gorel-version: PURL !eco-version: PURL </code></pre> </div> <h3 id="gaf-fields">GAF fields</h3> <p>The annotation flat file format is comprised of 17 tab-delimited fields.</p> <table> <thead> <tr> <th><strong>Column</strong></th> <th><strong>Content</strong></th> <th><strong>Required?</strong></th> <th><strong>Cardinality</strong></th> <th><strong>Example</strong></th> <th> </th> </tr> </thead> <tbody> <tr> <td>1</td> <td><a href="#db-column-1" title="Definition and requirements for DB (column 1)">DB</a></td> <td>required</td> <td>1</td> <td>UniProtKB</td> <td> </td> </tr> <tr> <td>2</td> <td><a href="#db-object-id-column-2" title="Definition and requirements for DB Object ID (column 2)">DB Object ID</a></td> <td>required</td> <td>1</td> <td>P12345</td> <td> </td> </tr> <tr> <td>3</td> <td><a href="#db-object-symbol-column-3" title="Definition and requirements for DB Object Symbol (column 3)">DB Object Symbol</a></td> <td>required</td> <td>1</td> <td>PHO3</td> <td> </td> </tr> <tr> <td>4</td> <td><a href="#relation-column-4" title="Definition and requirements for Relation (column 4)">Relation</a></td> <td>required</td> <td>1 or 2</td> <td>NOT|involved_in</td> <td> </td> </tr> <tr> <td>5</td> <td><a href="#go-id-column-5" title="Definition and requirements for GO ID (column 5)">GO ID</a></td> <td>required</td> <td>1</td> <td>GO:0003993</td> <td> </td> </tr> <tr> <td>6</td> <td><a href="#dbreference-column-6" title="Definition and requirements for DB:Reference (column 6)">DB:Reference (|DB:Reference)</a></td> <td>required</td> <td>1 or greater</td> <td>PMID:2676709</td> <td> </td> </tr> <tr> <td>7</td> <td><a href="#evidence-code-column-7" title="Definition and requirements for Evidence Code (column 7)">Evidence Code</a></td> <td>required</td> <td>1</td> <td>IMP</td> <td> </td> </tr> <tr> <td>8</td> <td><a href="#with-or-from-column-8" title="Definition and requirements for With [or] From (column 8)">With (or) From</a></td> <td>optional</td> <td>0 or greater</td> <td>GO:0000346</td> <td> </td> </tr> <tr> <td>9</td> <td><a href="#aspect-column-9" title="Definition and requirements for Aspect (column 9)">Aspect</a></td> <td>required</td> <td>1</td> <td>F</td> <td> </td> </tr> <tr> <td>10</td> <td><a href="#db-object-name-column-10" title="Definition and requirements for DB Object Name (column 10)">DB Object Name</a></td> <td>optional</td> <td>0 or 1</td> <td>Toll-like receptor 4</td> <td> </td> </tr> <tr> <td>11</td> <td><a href="#db-object-synonym-column-11" title="Definition and requirements for DB Object Synonym (column 11)">DB Object Synonym (|Synonym)</a></td> <td>optional</td> <td>0 or greater</td> <td>hToll</td> <td>Tollbooth</td> </tr> <tr> <td>12</td> <td><a href="#db-object-type-column-12" title="Definition and requirements for DB Object Type (column 12)">DB Object Type</a></td> <td>required</td> <td>1</td> <td>protein</td> <td> </td> </tr> <tr> <td>13</td> <td><a href="#taxon-column-13" title="Definition and requirements for Taxon (column 13)">Taxon(|taxon)</a></td> <td>required</td> <td>1 or 2</td> <td>taxon:9606</td> <td> </td> </tr> <tr> <td>14</td> <td><a href="#date-column-14" title="Definition and requirements for Date (column 14)">Date</a></td> <td>required</td> <td>1</td> <td>20090118</td> <td> </td> </tr> <tr> <td>15</td> <td><a href="#assigned-by-column-15" title="Definition and requirements for Assigned By (column 15)">Assigned By</a></td> <td>required</td> <td>1</td> <td>SGD</td> <td> </td> </tr> <tr> <td>16</td> <td><a href="#annotation-extension-column-16" title="Definition and requirements for Annotation Extension (column 16)">Annotation Extension</a></td> <td>optional</td> <td>0 or greater</td> <td>part_of(CL:0000576)</td> <td> </td> </tr> <tr> <td>17</td> <td><a href="#gene-product-form-id-column-17" title="Definition and requirements for Gene Product Form ID (column 17)">Gene Product Form ID</a></td> <td>optional</td> <td>0 or 1</td> <td>UniProtKB:P12345-2</td> <td> </td> </tr> </tbody> </table> <h3 id="definitions-and-requirements-for-field-contents">Definitions and requirements for field contents</h3> <h4 id="db-column-1">DB (column 1)</h4> <p>Refers to the database from which the identifier in <strong>DB object ID</strong> (column 2) is drawn. This is not necessarily the group submitting the file. If a UniProtKB ID is the <strong>DB object ID</strong> (column 2), <strong>DB</strong> (column 1) should be UniProtKB.</p> <p>Must be one of the values from the set of <a href="http://amigo.geneontology.org/xrefs">GO database cross-references</a>.</p> <div class="highlighter-rouge"><pre class="highlight"><code>This field is mandatory, cardinality 1. </code></pre> </div> <h4 id="db-object-id-column-2">DB Object ID (column 2)</h4> <p>A unique identifier from the database in DB (column 1) for the item being annotated.</p> <div class="highlighter-rouge"><pre class="highlight"><code>This field is mandatory, cardinality 1. </code></pre> </div> <p>Note that the identifier <strong>must reference a top-level primary gene or gene product identifier</strong>: either a gene, or a protein that has a 1:1 correspondence to a gene. Identifiers referring to particular protein isoforms or post-translationally cleaved or modified proteins are <em>not</em> legal values in this field.</p> <p>The <strong>DB object ID</strong> is the identifier for the database object, which may or may not correspond exactly to what is described in a paper. For example, a paper describing a protein may support annotations to the gene encoding the protein (gene ID in <strong>DB object ID</strong> field) or annotations to a protein object (protein ID in <strong>DB object ID</strong> field).</p> <h4 id="db-object-symbol-column-3">DB Object Symbol (column 3)</h4> <p>A (unique and valid) symbol to which <strong>DB object ID</strong> is matched. Can use ORF name for otherwise unnamed gene or protein. If gene products are annotated, can use gene product symbol if available, or many gene product annotation entries can share a gene symbol.</p> <div class="highlighter-rouge"><pre class="highlight"><code>This field is mandatory, cardinality 1. </code></pre> </div> <p>The <strong>DB Object Symbol</strong> field should be a symbol that means something to a biologist wherever possible (a gene symbol, for example). It is not an ID or an accession number (<strong>DB object ID</strong> [column 2] provides the unique identifier), although IDs can be used as a <strong>DB Object Symbol</strong> if there is no more biologically meaningful symbol available (e.g., when an unnamed gene is annotated).</p> <h4 id="relation-column-4">Relation (column 4)</h4> <p>Also referred to as <strong>Qualifier</strong> column. This column is populated with relations from the <a href="https://ontobee.org/ontology/RO">Relation Ontology</a> that describe how a gene product relates to the GO term with which it is associated. <a href="https://wiki.geneontology.org/Elements_of_an_annotation#Negation"><strong>Negation</strong></a> is represented by prepending “NOT” to a relation with a pipe.</p> <div class="highlighter-rouge"><pre class="highlight"><code>This field is mandatory in GAF 2.2; cardinality 1 or 2; for cardinality 2 use a pipe to separate the "NOT" from the relation (e.g. "NOT|contributes_to"). </code></pre> </div> <p><strong>If no relation is provided by a contributing group, default values (shown in bold below) will be added during file processing in the GO Central pipeline. The default relation represents the most general relation.</strong></p> <p>See also the <a href="http://geneontology.org/docs/go-annotations/#annotation-qualifiers">documentation on qualifiers</a> in the GO annotation guide.</p> <table> <thead> <tr> <th><strong>GO Aspect</strong></th> <th> <strong>Default relation</strong></th> <th> <strong>Default relation for root annotations</strong></th> <th> <strong>Other allowed relations</strong></th> </tr> </thead> <tbody> <tr> <td><strong>Molecular Function</strong></td> <td><a href="https://wiki.geneontology.org/Enables"><strong>enables</strong></a></td> <td> <a href="https://wiki.geneontology.org/Enables">enables</a></td> <td> <a href="https://wiki.geneontology.org/Contributes_to">contributes_to</a></td> </tr> <tr> <td> <strong>Biological Process</strong></td> <td> <a href="https://wiki.geneontology.org/Acts_upstream_of_or_within"><strong>acts_upstream_of_or_within</strong></a></td> <td> <a href="https://wiki.geneontology.org/Involved_in">involved_in</a></td> <td><a href="https://wiki.geneontology.org/Acts_upstream_of">acts_upstream_of</a>, <a href="https://wiki.geneontology.org/Acts_upstream_of,_positive_effect">acts_upstream_of_positive_effect</a>, <a href="https://wiki.geneontology.org/Acts_upstream_of,_negative_effect">acts_upstream_of_negative_effect</a>, <a href="https://wiki.geneontology.org/Acts_upstream_of_or_within,_negative_effect">acts_upstream_of_or_within_negative_effect</a>, <a href="https://wiki.geneontology.org/Acts_upstream_of_or_within,_positive_effect">acts_upstream_of_or_within_positive_effect</a></td> </tr> <tr> <td><strong>Cellular Component</strong></td> <td> <a href="http://purl.obolibrary.org/obo/RO_0001025"><strong>located_in</strong> </a> for <a href="http://amigo.geneontology.org/amigo/term/GO:0110165">cellular anatomical entity</a> and <a href="http://amigo.geneontology.org/amigo/term/GO:0044423#display-lineage-tab">virion component</a> & children and <a href="https://wiki.geneontology.org/Part_of_relation"><strong>part_of</strong></a> for <a href="GO:0032991 protein-containing complex">protein-containing complex</a> & children</td> <td> <a href="https://wiki.geneontology.org/Is_active_in">is_active_in</a></td> <td> <a href="https://wiki.geneontology.org/Colocalizes_with">colocalizes_with</a></td> </tr> </tbody> </table> <h4 id="go-id-column-5">GO ID (column 5)</h4> <p>The GO identifier for the term attributed to the <strong>DB object ID</strong>.</p> <div class="highlighter-rouge"><pre class="highlight"><code>This field is mandatory, cardinality 1. </code></pre> </div> <h4 id="dbreference-column-6">DB:Reference (column 6)</h4> <p>One or more unique identifiers for a single source cited as an authority for the attribution of the <strong>GO ID</strong> to the <strong>DB Object ID</strong>. This may be a literature reference or a database record. The syntax is DB:accession_number.</p> <p>Note that <strong>only one reference can be cited on a single line</strong> in the gene association file. If a reference has identifiers in more than one database, multiple identifiers for that reference can be included on a single line. For example, if the reference is a published paper that has a PubMed ID, we strongly recommend that the PubMed ID be included, as well as an identifier within a model organism database. Note that if the model organism database has an identifier for the reference, that identifier should <strong>always</strong> be included, even if a PubMed ID is also used</p> <div class="highlighter-rouge"><pre class="highlight"><code>This field is mandatory, cardinality 1, >1; for cardinality >1 use a pipe to separate entries (e.g. SGD_REF:S000047763|PMID:2676709). </code></pre> </div> <h4 id="evidence-code-column-7">Evidence Code (column 7)</h4> <p>See the <a href="http://geneontology.org/page/guide-go-evidence-codes">GO evidence code guide</a> for the list of valid evidence codes for GO annotations</p> <div class="highlighter-rouge"><pre class="highlight"><code>This field is mandatory, cardinality 1. </code></pre> </div> <h4 id="with-or-from-column-8">With [or] From (column 8)</h4> <p>Also referred to as <strong>With, From</strong> or the <strong>With/From</strong> column. This field is used to hold an additional identifier for annotations, for example, it can identify another gene product to which the annotated gene product is similar (ISS) or interacts with (IPI). An entry in the <strong>With/From</strong> field is <em>not</em> allowed for annotations made using the following evidence codes: EXP, IDA, IEP, TAS, NAS, ND. However, population of the <strong>With/From</strong> is mandatory for certain evidence codes, see the documentation for the individual evidence codes for more information.</p> <p>Some permitted values are:</p> <div class="highlighter-rouge"><pre class="highlight"><code> DB:gene_symbol DB:gene_symbol[allele_symbol] DB:gene_id DB:protein_name DB:sequence_id GO:GO_id CHEBI:CHEBI_id IntAct:Complex _id RNAcentral:RNAcentral_id more... </code></pre> </div> <p>Multiple entries are allowed in the <strong>With/From</strong> field of certain evidence codes (see below) and they must be separated with a pipe or a comma. The pipe (|) specifies an independent statement (OR) and is equivalent to making separate annotations, i.e. not all conditions are required to infer the annotated GO term. The comma (,) specifies a connected statement (AND) and indicates that all conditions are required to infer the annotated GO term. In this case, ‘OR’ is a weaker statement than ‘AND’, therefore will be correct in all cases. Pipe and comma separators may be used together in the same <strong>With/From</strong> field.</p> <div class="highlighter-rouge"><pre class="highlight"><code>This field is required for some evidence codes (see below or evidence code documentation); cardinality 0, 1, >1. </code></pre> </div> <p>The <strong>With/From</strong> field may be populated with multiple identifiers when making annotations using the following evidence codes: IMP, IGI, IPI, IC, ISS, ISA, ISO, ISM, IGC, IBA, IKR, RCA, IEA.</p> <p>Annotations made using the following evidence codes may only use the pipe operator in the <strong>With/From</strong> field: ISS, ISA, ISO, ISM, IBA, IKR, RCA, IEA. It is not mandatory to use pipes, however, and some groups may prefer to make separate annotations.</p> <p>Annotations made using the following evidence codes may use the pipe or comma operators in the <strong>With/From</strong> field: IMP, IGI, IPI, IC, IGC.</p> <h5 id="examples">Examples</h5> <ol> <li>Recording gene IDs for allelic variations in the With/from column for IMP evidence code: Multiple pipe-separated values in the <strong>With/From</strong> field indicate that the process is inferred from each perturbation independently. If more than one variation within the same locus resulted in a phenotype, those variations should be comma-separated (implying AND). For e.g. Two different deletion mutations and one RNAi inactivation support the same GO annotation for a Worm gene. The alleles are Pipe-separated in the <strong>With/From</strong> for this annotation: WB:WBVariation00091989|WB:WBVar00249869|WB:WBRNAi00084583.</li> <li>Recording gene IDs for mutants in the <strong>With/From</strong> column for IGI evidence code: Pipe-separated (OR) values should be used to indicate individual genetic interactions that result in the same inference for a process. Multiple values indicating triple mutants, for example, should be comma-separated (AND). For e.g. A triple mutant in C. elegans supports annotation to a specific process using IGI evidence. The gene identifiers are comma-separated in the <strong>With/From</strong> for this annotation indicating that the process is inferred from all three genes together: WBGene00000035,WBGene00000036.</li> <li>Recording IDs in the <strong>With/From</strong> column for IEA evidence code: Multiple, pipe-separated InterPro accessions are used for IEA-based annotations in the UniProt files and indicate individual (unconnected) inferences. For e.g. annotations to cell redox homeostasis (GO:0045454) that are inferred from three InterPro domains: InterPro:IPR005746|InterPro:IPR013766|InterPro:IPR017937.</li> </ol> <p>This removes a large amount of redundancy and significantly decreases the size of UniProt files.</p> <p>Note that a gene ID may be used in the <strong>With/From</strong> column for a IPI annotation, or for an ISS annotation based on amino acid sequence or protein structure similarity, if the database does not have identifiers for individual gene products. A gene ID may also be used if the cited reference provides enough information to determine which gene ID should be used, but not enough to establish which protein ID is correct.</p> <p>‘GO:GO_id’ is used only when the evidence code is IC, and refers to the GO term(s) used as the basis of a curator inference. In these cases the entry in the ‘DB:Reference’ column will be that used to assign the GO term(s) from which the inference is made. The <strong>With/From</strong> is mandatory for evidence code IC.</p> <p>The ID used in the <strong>With/From</strong> field should be an identifier for an individual entry in a database (such as a sequence ID, gene ID, GO ID, etc.). Identifiers from the Center for Biological Sequence Analysis (CBS), however, represent tools used to find homology or sequence similarity; these identifiers should not be used in the <strong>With/From</strong> column.</p> <h4 id="aspect-column-9">Aspect (column 9)</h4> <p>Refers to the namespace or ontology to which the <strong>GO ID</strong> (column 5) belongs; one of P (biological process), F (molecular function) or C (cellular component).</p> <div class="highlighter-rouge"><pre class="highlight"><code>This field is mandatory; cardinality 1. </code></pre> </div> <h4 id="db-object-name-column-10">DB Object Name (column 10)</h4> <p>Name of gene or gene product.</p> <div class="highlighter-rouge"><pre class="highlight"><code>This field is not mandatory, cardinality 0, 1 [white space allowed]. </code></pre> </div> <h4 id="db-object-synonym-column-11">DB Object Synonym (column 11)</h4> <p>Gene symbol [or other text] Note that we strongly recommend that gene synonyms are included in the gene association file, as this aids the searching of GO.</p> <div class="highlighter-rouge"><pre class="highlight"><code>This field is not mandatory, cardinality 0, 1, >1 [white space allowed]; for cardinality >1 use a pipe to separate entries (e.g. YFL039C|ABY1|END7|actin gene). </code></pre> </div> <h4 id="db-object-type-column-12">DB Object Type (column 12)</h4> <p>A description of the type of gene product being annotated. If a <strong>Gene Product Form ID</strong> (column 17) is supplied, the <strong>DB Object Type</strong> will refer to that entity; if no <strong>Gene Product Form ID</strong> is present, it will refer to the entity that the <strong>DB Object Symbol</strong> (column 2) is believed to produce and which actively carries out the function or localization described. <strong>DB Object Type</strong> will be one of the following: protein_complex; protein; transcript; ncRNA; rRNA; tRNA; snRNA; snoRNA; any subtype of ncRNA in the <a href="http://www.sequenceontology.org/browser/obob.cgi">Sequence Ontology</a>. If the precise product type is unknown, gene_product should be used.</p> <div class="highlighter-rouge"><pre class="highlight"><code>This field is mandatory, cardinality 1. </code></pre> </div> <p>The object type (gene_product, transcript, protein, protein_complex, etc.) listed in the <strong>DB Object Type</strong> field must match the database entry identified by the <strong>Gene Product Form ID</strong>, or, if this is absent, the expected product of the <strong>DB Object ID</strong>. Note that <strong>DB Object Type</strong> refers to the database entry (i.e. it represents a protein, functional RNA, etc.); this column does not reflect anything about the GO term or the evidence on which the annotation is based. For example, if your database entry represents a protein-encoding gene, then protein goes in the <strong>DB Object Type</strong> column. The text entered in the <strong>DB Object Name</strong> and <strong>DB Object Symbol</strong> should refer to the entity in <strong>DB Object ID</strong>. For example, several alternative transcripts from one gene may be annotated separately, each with the same gene ID in <strong>DB Object ID</strong>, and specific gene product identifiers in <strong>Gene Product Form ID</strong>, but list the same gene symbol in the <strong>DB Object Symbol</strong> column.</p> <h4 id="taxon-column-13">Taxon (column 13)</h4> <p>Taxonomic identifier(s).</p> <p>For cardinality 1, the ID of the species encoding the gene product.</p> <p>For cardinality 2, to be used only in conjunction with terms that have the biological process term ‘GO:0044419 biological process involved in interspecies interaction between organisms’ or the cellular component term ‘GO:0018995 host cellular component’ as an ancestor. The first taxon ID should be that of the organism encoding the gene or gene product, and the taxon ID after the pipe should be that of the other organism in the interaction</p> <div class="highlighter-rouge"><pre class="highlight"><code>This field is mandatory, cardinality 1, 2; for cardinality 2 use a pipe to separate entries (e.g. taxon:1|taxon:1000). </code></pre> </div> <p>See the <a href="http://geneontology.org/page/go-annotation-conventions#interactions">GO annotation conventions for more information on multi-organism terms</a>.</p> <h4 id="date-column-14">Date (column 14)</h4> <p>Date on which the annotation was made; format is YYYYMMDD.</p> <div class="highlighter-rouge"><pre class="highlight"><code>This field is mandatory, cardinality 1. </code></pre> </div> <h4 id="assigned-by-column-15">Assigned By (column 15)</h4> <p>The database which made the annotation.</p> <p>One of the values from the set of GO database cross-references.</p> <p>Used for tracking the source of an individual annotation. Default value is value entered as the <strong>DB</strong>(column 1). Value will differ from column 1 for any annotation that is made by one database and incorporated into another.</p> <div class="highlighter-rouge"><pre class="highlight"><code>This field is mandatory, cardinality 1. </code></pre> </div> <h4 id="annotation-extension-column-16">Annotation Extension (column 16)</h4> <p>One of:</p> <div class="highlighter-rouge"><pre class="highlight"><code> DB:gene_id DB:sequence_id CHEBI:CHEBI_id Cell Type Ontology:CL_id GO:GO_id </code></pre> </div> <p>Contains cross references to other ontologies that can be used to qualify or enhance the annotation. The cross-reference is prefaced by an appropriate GO relationship; references to multiple ontologies can be entered. For example, if a gene product is localized to the mitochondria of lymphocytes, the <strong>GO ID</strong> (column 5) would be mitochondrion ; GO:0005739, and the annotation extension column would contain a cross-reference to the term lymphocyte from the Cell Type Ontology.</p> <p>Targets of certain processes or functions can also be included in this field to indicate the gene, gene product, or chemical involved; for example, if a gene product is annotated to protein kinase activity, the annotation extension column would contain the UniProtKB protein ID for the protein phosphorylated in the reaction.</p> <p>The pipe (|) specifies an independent statement (OR) and is equivalent to making separate annotations, i.e. not all conditions are required to infer the annotated GO term. The comma (,) specifies a connected statement (AND) and indicates that all conditions are required to infer the annotated GO term. In this case, ‘OR’ is a weaker statement than ‘AND’, therefore will be correct in all cases. Pipe and comma separators may be used together in the same <strong>Annotation Extension</strong> field.</p> <p>See the documentation on using the <strong>Annotation Extension</strong> column for details of practical usage; a wider discussion of the annotation extension column can be found on the <a href="http://wiki.geneontology.org/index.php/Annotation_Extension">GO internal documentation site</a>.</p> <div class="highlighter-rouge"><pre class="highlight"><code>This field is optional, cardinality 0, 1, >1. </code></pre> </div> <h4 id="gene-product-form-id-column-17">Gene Product Form ID (column 17)</h4> <p>As the <strong>DB Object ID</strong> (column 2) entry must be a canonical entity—a gene OR an abstract protein that has a 1:1 correspondence to a gene—this field allows the annotation of specific variants of that gene or gene product. Contents will frequently include protein sequence identifiers: for example, identifiers that specify distinct proteins produced by to differential splicing, alternative translational starts, post-translational cleavage or post-translational modification. Identifiers for functional RNAs can also be included in this column.</p> <p>The identifier used must be a standard 2-part global identifier, e.g. UniProtKB:OK0206-2</p> <ul> <li>When the <strong>Gene Product Form ID</strong> is filled with a protein identifier, the value in <strong>DB Object Type</strong> (column 12) must be protein. Protein identifiers can include UniProtKB accession numbers, NCBI NP identifiers or Protein Ontology (PRO) identifiers.</li> <li>When the <strong>Gene Product Form ID</strong> is filled with a functional RNA identifier, the <strong>DB Object Type</strong> (column 12) must be either ncRNA, rRNA, tRNA, snRNA, or snoRNA</li> </ul> <p>This column may be left blank; if so, the value in <strong>DB Object Type</strong> (column 12) will provide a description of the expected gene product.</p> <p>More information and examples are available from the <a href="http://wiki.geneontology.org/index.php/GAF_Col17_GeneProducts">GO internal documentation on column 17</a>. Note that several fields contain database cross-reference (dbxrefs) in the format dbname:dbaccession. The fields are: <strong>GO ID</strong> [column 5], where dbname is always GO; <strong>DB:Reference</strong> (column 6); <strong>With or From</strong> (column 8); and <strong>Taxon</strong> (column 13), where dbname is always taxon. For <strong>GO ID</strong>s, do not repeat the ‘GO:’ prefix (i.e. always use GO:0000000, not GO:GO:0000000).</p> </article> </div> </div> </div> </div> <footer class="footer"> <hr style="margin:8px; padding:0px"> <div > <div class="col-sm-5" style="padding-left: 45px; text-align: left;"> <div class="footer__navigation"> <ul class="footer__list" style="padding-left: 0px;"> <li class="footer__item"> <a href="/" class="footer__link link-extended" style="color: white !important;">Home</a> </li> <li class="footer__item"> <a href="https://help.geneontology.org" class="footer__link link-extended" style="color: white !important;" target="blank">Contact us</a> </li> <li class="footer__item"> <a href="/docs/go-citation-policy/" class="footer__link link-extended" style="color: white !important;">Citation and Terms of Use</a> </li> </ul> </div> </div> <div class="col-sm-2" style="padding-left: 45px; padding-right: 45px; text-align: center;"> <div class="footer__logo-list"> <a href="https://globalbiodata.org/scientific-activities/global-core-biodata-resources" target="blank" alt="Global Core Biodata Resource" > <img src="/assets/GCBR-Logo-White.png" alt="Global Core Biodata Resource" style="height: 60px;"/> </a> </div> </div> <div class="col-sm-5" style="padding-left: 0px; padding-right: 35px; text-align: right;"> <p class="footer__copyright"> <small class="footer__text"> Copyright © 1999-2024 Member of the <a href="https://obofoundry.org/" class="footer__link" rel="external" title="Open Biological Ontologies" target="blank">Open Biological Ontologies Foundry</a> The GO Consortium is funded by the National Human Genome Research Institute (US National Institutes of Health), grant number <a href="https://reporter.nih.gov/search/BqfmFvQGv0CWrEFOkzTp-w/project-details/10348001" class="footer__link" rel="external" title="HG012212"target="blank">HG012212</a>, with co-funding by NIGMS. </small> </p> </div> </div> </footer> <script> var baseurl = '' </script> <script src="//code.jquery.com/jquery-1.10.2.min.js"></script> <script src="/js/bootstrap.min.js "></script> <script src="/js/typeahead.bundle.min.js "></script> <script src="/js/main.js "></script> </body> </html>