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Merge pull request #682 from geneontology/pgaudet-patch-85
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Update gene-product-information-gpi-format-20.md
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pgaudet authored Dec 6, 2024
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Expand Up @@ -21,20 +21,19 @@ Mandatory elements of the GPI 2.0 file header are:
- the name of database or group generating the file, as listed in [dbxrefs.yaml file](https://github.com/geneontology/go-site/blob/master/metadata/db-xrefs.yaml)
- the date the file was generated conforming to the date portion of [ISO 8601](https://www.iso.org/iso-8601-date-and-time-format.html) standards, i. e. `YYYY-MM-DD`
- Example GPI 2.0 header:


```
!gpi-version: 2.0
!generated-by: SGD
!date-generated: 2024-05-01

```
- Additional information may also be included, for example project URL and funding sources. For example:

```
!URL: http://www.yeastgenome.org/
!Project-release: WS275
!Funding: NHGRI grant number HG012212
```
## GPI file fields

## GPI File Contents
The GPI 2.0 file comprises 11 tab-delimited fields. For fields that multiple values, those should be separated by pipes (`|`).
**Required fields are shown with an asterisk (*).**
Expand All @@ -52,84 +51,64 @@ The GPI 2.0 file comprises 11 tab-delimited fields. For fields that multiple val
| 10 | [Cross-reference(s)](#10-db-xrefs "Definition and requirements for DB_Xref(s) (column 10)") | 0 or > | NCBIGene:154796 \|<br/>ENSEMBL:ENSG00000126016 | NCBIGene:154796 \|<br/>ENSEMBL:ENSG00000126016 | ComplexPortal:CPX-1016 | UniProtKB:Q9DAQ4-1 | ENSG00000276365 | 
| 11 | [Gene Product Properties](#11-gene-product-properties "Definition and requirements for Gene Product Properties (column 11)") | 0 or > | db_subset=Swiss-Prot| | | | 
### Definitions and requirements for field contents

### Definitions and requirements for GPI 2.0 field contents
#### 1. DB:Object ID
* A unique identifier for the entity being annotated, composed of two elements: a **DB** prefix is the database, that must be described in the GO [dbxrefs.yaml file](https://github.com/geneontology/go-site/blob/master/metadata/db-xrefs.yaml), and a **DB Object ID**, which is the alphanumerical identifier corresponding to the entity. The **DB:DB Object ID** is the combined identifier for the database object. Examples:

UniProtKB:P99999
SGD:S000002164
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.

+ UniProtKB:P99999
+ SGD:S000002164
+ 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.

* 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.

* 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.

* 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
* [GO:0032991](http://purl.obolibrary.org/obo/PR_000000001): protein-containing complex
* [SO:0001217](http://purl.obolibrary.org/obo/SO_0001217): protein-coding gene
* [SO:0000704](http://purl.obolibrary.org/obo/SO_0000704): gene
* [SO:0000655](http://purl.obolibrary.org/obo/SO_0000655): ncRNA or any SO child term
* [SO:0001263](http://purl.obolibrary.org/obo/SO_0001263): ncRNA-coding gene or any SO child term

**Note on object types**: This field should descibe the type of biological object as defined by the contributing database. For example, [WormBase identifiers](https://wormbase.org/species/c_elegans/gene/WBGene00000001) represent [genes](http://purl.obolibrary.org/obo/SO_0000704), PomBase identifiers represent [protein-coding genes](http://purl.obolibrary.org/obo/SO_0001217), and [SGD identifiers](https://www.yeastgenome.org/locus/S000002429) represent [proteins](http://purl.obolibrary.org/obo/PR_000000001).

GO strongly recommends against using 'gene' or 'gene product' as this does not allow to differentiate between proteins and ncRNAs.

* 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
* [GO:0032991](http://purl.obolibrary.org/obo/PR_000000001): protein-containing complex
* [SO:0001217](http://purl.obolibrary.org/obo/SO_0001217): protein-coding gene
* [SO:0000704](http://purl.obolibrary.org/obo/SO_0000704): gene
* [SO:0000655](http://purl.obolibrary.org/obo/SO_0000655): ncRNA or any SO child term
* [SO:0001263](http://purl.obolibrary.org/obo/SO_0001263): ncRNA-coding gene or any SO child term
* **Note on object types**: This field should descibe the type of biological object as defined by the contributing database. For example, [WormBase identifiers](https://wormbase.org/species/c_elegans/gene/WBGene00000001) represent [genes](http://purl.obolibrary.org/obo/SO_0000704), PomBase identifiers represent [protein-coding genes](http://purl.obolibrary.org/obo/SO_0001217), and [SGD identifiers](https://www.yeastgenome.org/locus/S000002429) represent [proteins](http://purl.obolibrary.org/obo/PR_000000001).
* GO strongly recommends against using 'gene' or 'gene product' as this does not allow to differentiate between proteins and ncRNAs.
<!---
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`.

* 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.

* 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.

* 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, > 1; for cardinality >1, values must be pipe-separated.
<!---
How can that be??? this should be 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.

* 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.

* 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).

* 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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