From b275bf62021d009bb2c98f749778961134b9b89f Mon Sep 17 00:00:00 2001 From: suzialeksander Date: Tue, 10 Dec 2024 14:11:42 -0700 Subject: [PATCH] Update gene-product-information-gpi-format-20.md formatting --- .../gene-product-information-gpi-format-20.md | 20 +++++++++---------- 1 file changed, 10 insertions(+), 10 deletions(-) diff --git a/_docs/gene-product-information-gpi-format-20.md b/_docs/gene-product-information-gpi-format-20.md index 07b00dbf..9de5c3f3 100644 --- a/_docs/gene-product-information-gpi-format-20.md +++ b/_docs/gene-product-information-gpi-format-20.md @@ -59,20 +59,20 @@ The GPI 2.0 file comprises 11 tab-delimited fields. For fields that multiple val + MGI:MGI:1919306 * The identifier may reference the canonical form of a gene or gene product including functional RNAs, as well as gene variants, distinct proteins produced by to differential splicing, alternative translational starts, post-translational cleavage or post-translational modification. If the gene product is not a canonical gene or gene product identifier, the corresponding canonical form must be referenced in Column 8 (Parent Protein) of the GPI file. * Cardinality = 1 ---- + #### 2. Object Symbol * The unique symbol corresponding to the **DB:Object_ID** in Column 1; usually the name of the gene. No white spaces allowed. * The symbol is not a unique identifier or an accession number (unlike the **DB:Object_ID**), but if the entity does not have a symbol, the **DB:Object_ID** may be used as **Object Symbol**. For example, several alternative transcripts from one gene may be annotated separately, each with specific gene product identifiers in **DB:Object_ID**, but with the same gene symbol in the **Object_Symbol** column. * Cardinality = 1 ---- + #### 3. Object Name * The name of the gene or gene product corresponding to the **DB:Object_ID** in Column 1. White spaces are allowed in this field. * Cardinality = 0 or 1 ---- + #### 4. Object Synonym * Alternative names for the entity in **DB:Object_ID** in Column 1. These entries may be a gene symbol, clone ID, or any other label ot identifier. Object synonyms are useful for searching. * Cardinality = 0, 1, > 1; for cardinality > 1, values must be pipe-separated. ---- + #### 5. Object Type * An ontology identifier describing the class of biological entity of the **DB:Object_ID** in Column 1. The ontology identifier must be a value from Protein Ontology for proteins, Gene Ontology for protein complexes, or Sequence Ontology for all other entities. Allowed entity types: * [PR:000000001](http://purl.obolibrary.org/obo/PR_000000001): protein @@ -86,27 +86,27 @@ The GPI 2.0 file comprises 11 tab-delimited fields. For fields that multiple val * Cardinality = 1 ---- + #### 6. Object Taxon * The [NCBI taxon ID](https://www.ncbi.nlm.nih.gov/taxonomy) of the organism (species or strain) encoding the **DB:Object_ID** from Column 1, in the format `NCBITaxon:numerical_identifier`. * Cardinality = 1 ---- + #### 7. Encoded by * For proteins and transcripts, **Encoded by** refers to the gene ID that encodes those entities, e.g. ENSG00000197153. * Cardinality = 0, 1, > 1; for cardinality > 1, values must be pipe-separated. ---- + #### 8. Parent Protein * When the **DB:Object_ID** in Column 1 describes a protein isoform or a modified protein, this column refers to the gene-centric reference protein accession of the column 1 entry. * Cardinality = 0, 1 ---- + #### 9. Protein-Containing Complex Members * When the **DB:Object_ID** in Column 1 describes a protein-containing complex, this column contains the gene-centric reference protein accessions. * Cardinality = 0, 1, > 1; for cardinality > 1, values must be pipe-separated. ---- + #### 10. Database cross-references (DB_Xrefs) * Identifiers for the object in **DB:Object_ID** found in other databases. Identifiers used must be standard 2-part global identifiers, e.g. UniProtKB:Q60FP0. For proteins in model organism databases, **DB_Xrefs** must include the correponding UniProtKB ID, and may also include NCBI gene or protein IDs, etc. * Cardinality = 0, 1, > 1; for cardinality > 1, values must be pipe-separated. ---- + #### 11. Gene Product Properties * The Properties column can be filled with a pipe separated list of values in the format "property_name = property_value". There is a fixed vocabulary for the property names and this list can be extended when necessary. Supported properties will include: 'GO annotation complete', "Phenotype annotation complete' (the value for these two properties would be a date), 'Target set' (e.g. Reference Genome, kidney, etc.), 'Database subset' (e.g. Swiss-Prot, TrEMBL). * Cardinality = 0, 1, > 1; for cardinality > 1, values must be pipe-separated.