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Update gene-product-information-gpi-format-20.md
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suzialeksander authored Dec 10, 2024
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Expand Up @@ -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
Expand All @@ -86,27 +86,27 @@ The GPI 2.0 file comprises 11 tab-delimited fields. For fields that multiple val
<!---
SGD feature type named ORF in SGD --->
* 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.

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