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Merge pull request #546 from geneontology/suzialeksander-patch-114
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Update gene-product-information-gpi-format-20.md
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suzialeksander authored May 30, 2024
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30 changes: 14 additions & 16 deletions _docs/gene-product-information-gpi-format-20.md
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Expand Up @@ -47,16 +47,16 @@ The file format comprises 11 tab-delimited fields. Fields with multiple values (

| **Column** | **Content** | **Required?** | **Cardinality** | **Example**|
|----------|---------|-------------|---------|--------|
| 1 | [DB:DB_Object_ID](#dbdb-object-id "Definition and requirements for DB:DB Object ID (column 1)") | required | 1 | UniProtKB:Q4VCS5|
| 1 | [DB:DB_Object_ID](#dbdb-object-id "Definition and requirements for DB:DB Object ID (column 1)") | required | 1 | UniProtKB:Q4VCS5-1|
| 2 | [DB_Object_Symbol](#db-object-symbol "Definition and requirements for DB Object Symbol (column 2)") | required | 1 | AMOT|
| 3 | [DB_Object_Name](#db-object-name "Definition and requirements for DB Object Name (column 3)") | optional | 0 or greater | Angiomotin|
| 4 | [DB_Object_Synonym(s)](#db-object-synonym "Definition and requirements for DB Object Synonym(s) (column 4)") | optional | 0 or greater | E230009N18Rik\|KIAA1071|
| 4 | [DB_Object_Synonym(s)](#db-object-synonym "Definition and requirements for DB Object Synonym(s) (column 4)") | optional | 0 or greater | KIAA1071|
| 5 | [DB_Object_Type](#db-object-type "Definition and requirements for DB Object Type (column 5)") | required | 1 | PR:000000001|
| 6 | [DB_Object_Taxon](#db-object-taxon "Definition and requirements for DB Object Taxon (column 6)") | required | 1 | NCBItaxon:9606|
| 7 | [Encoded_by](#encoded-by "Definition and requirements for Encoded by (column 7)") | optional | 0 or greater | ***EXAMPLE NEEDED***|
| 6 | [DB_Object_Taxon](#db-object-taxon "Definition and requirements for DB Object Taxon (column 6)") | required | 1 | NCBITaxon:9606|
| 7 | [Encoded_by](#encoded-by "Definition and requirements for Encoded by (column 7)") | optional | 0 or greater | HGNC:17810 |
| 8 | [Parent_Protein](#parent-protein "Definition and requirements for Parent Protein (column 8)") | optional | 0 or 1 | UniProtKB:Q4VCS5|
| 9 | [Protein_Containing_Complex_Members](#protein-containing-complex-members "Definition and requirements for Protein Containing Complex Members (column 9)") | optional | 0 or greater | SGD:S000003821,SGD:S000001456,SGD:S000005047|
| 10 | [DB_Xref(s)](#db-xrefs "Definition and requirements for DB_Xref(s) (column 10)") | optional | 0 or greater | ***EXAMPLE NEEDED*** |
| 10 | [DB_Xref(s)](#db-xrefs "Definition and requirements for DB_Xref(s) (column 10)") | optional | 0 or greater | NCBIGene:154796\|ENSEMBL:ENSG00000126016 |
| 11 | [Gene_Product_Properties](#gene-product-properties "Definition and requirements for Gene Product Properties (column 11)") | optional | 0 or greater | db_subset=Swiss-Prot|


Expand All @@ -65,7 +65,7 @@ The file format comprises 11 tab-delimited fields. Fields with multiple values (

SGD:S000217643 CBF1:MET4:MET28CBF1-MET4-MET28 sulfur metabolism transcription factor complex GO:0032991 NCBItaxon:559292 SGD:S000003821,SGD:S000001456,SGD:S000005047 ComplexPortal:CPX-1016

RNAcentral:URS0000C3938B_6185 Schistosoma haematobium Hammerhead ribozyme (type I) ribozyme sequence hammerhead_ribozyme NCBITaxon:6185
RNAcentral:URS0000527F89_9606 Homo sapiens (human) hsa-miR-145-5p SO:0000276 NCBITaxon:9606 HGNC:31532 NCBIGene:406937\|ENSEMBL:ENSG00000276365


### Definitions and requirements for field contents
Expand All @@ -87,7 +87,7 @@ The text entered in the **DB_Object_Symbol** should refer to the entity in **DB:
This field is mandatory, cardinality 1.

#### DB Object Name
The name of the gene or gene product in **DB:DB_Object_ID**. The text entered in the **DB_Object_Name** should refer to the entity in **DB:DBB_Object_ID**. White spaces are allowed in this field.
The name of the gene or gene product in **DB:DB_Object_ID**. The text entered in the **DB_Object_Name** should refer to the entity in **DB:DB_Object_ID**. White spaces are allowed in this field.

This field is not mandatory, cardinality 0, 1.

Expand All @@ -97,24 +97,22 @@ Alternative names for the entity in **DB:DB_Object_ID**. These entries may be a
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).

#### DB Object Type
An ontology identifier for the biological entity in **DB:DB_Object_ID** which is annotated with GO. This field uses Sequence Ontology, Protein Ontology, and GO IDs and must correspond to one of the [permitted GPI entity types](https://github.com/geneontology/go-annotation/blob/master/specs/gpad-gpi-2-0.md#gpi-entity-types) or a more granular child term. Acceptable entries include:
An ontology identifier for the biological entity in **DB:DB_Object_ID** which is annotated with GO. This field uses Sequence Ontology, Protein Ontology, and GO IDs and must correspond to one of the [permitted GPI entity types](https://github.com/geneontology/go-annotation/blob/master/specs/gpad-gpi-2-0.md#gpi-entity-types) or a more granular child term. Common entries include:

* protein PR:000000001
* protein-coding gene SO:0001217
* ncRNA-coding gene SO:0001263
* mRNA SO:0000234
* gene SO:0000704
* ncRNA SO:0000655
* protein PR:000000001
** any subtype of ncRNA in the Sequence Ontology, including ncRNA-coding gene SO:0001263
* protein-containing complex GO:0032991
* marker or uncloned locus SO:0001645
* any subtype of ncRNA in the Sequence Ontology

The object type (gene, transcript, protein, protein_complex, etc.) listed in the **DB_Object_Type** field must match the database entry identified by the **DB:DB_Object_ID**. Note that **DB_Object_Type** 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.
The object type listed in the **DB_Object_Type** field must match the database entry identified by the **DB:DB_Object_ID**.


This field is mandatory, cardinality 1.

#### DB Object Taxon
The NCBI taxon ID of the species encoding the gene product, specified as a number with the prefix `NCBItaxon:`.
The NCBI taxon ID of the species encoding the **DB:DB_Object_ID**, including the prefix `NCBItaxon:`.

This field is mandatory, cardinality 1.

Expand All @@ -134,7 +132,7 @@ When column 1 references a protein-containing complex, this column contains the
This field is optional, cardinality 0+; multiple identifiers should be pipe-separated.

#### DB Xrefs
Identifiers for the object in **DB:DB_Object_ID** found in other databases. Identifiers used must be standard 2-part global identifiers, e.g. UniProtKB:OK0206. For gene products in model organism databases, **DB_Xrefs** must include the UniProtKB ID, and may also include NCBI gene or protein IDs, etc.
Identifiers for the object in **DB:DB_Object_ID** found in other databases. Identifiers used must be standard 2-part global identifiers, e.g. UniProtKB:Q60FP0. For gene products in model organism databases, **DB_Xrefs** must include the UniProtKB ID, and may also include NCBI gene or protein IDs, etc.

This field is optional, cardinality 0+; multiple identifiers should be pipe-separated.

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