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Add comma-separation for Interacting_taxon_ID; add definition for Taxon_ID; add definition for Relation_ID #3171

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Jul 1, 2020
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Add comma-separation for Interacting_taxon_ID; add definition for Taxon_ID; add definition for Relation_ID #3171

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Add comma-separation for Interacting_taxon_ID; add definition for Tax…
balhoff Jul 1, 2020
9a1cea4
Use both pipe and comma for interacting taxon.
balhoff Jul 1, 2020
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9 changes: 8 additions & 1 deletion specs/gpad-gpi-2-0.md
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Original file line number Diff line number Diff line change
Expand Up @@ -73,6 +73,7 @@ GPI and GPAD documents consist of sequences of Unicode characters and are encode
| A |B |C |D |E |F |G |H |I |J |K |L |M |N |O |P |Q |R |S |T |U |V |W |X |Y |Z
Digit ::= 0 |1 |2 |3 |4 |5 |6 |7 |8 |9
Alphanumeric_Char ::= Alpha_Char | Digit
Alphanumeric ::= Alphanumeric_Char+

### Spacing Characters

Expand Down Expand Up @@ -196,16 +197,22 @@ Each annotation is on a separate line of tab separated values:
5 | Reference ::= [ID] ('\|' ID)* | | 1 or greater | PMID:30695063 | Different IDs, e.g. PMID and MOD paper id, must correspond to the same publication or reference
6 | Evidence_type ::= OBO_ID | Evidence and Conclusion Ontology | 1 | ECO:0000315 | Mapping file in progress: https://github.com/evidenceontology/evidenceontology/issues/249
7 | With_or_From ::= [ID] ('\|' \| ‘,’ ID)* | | 0 or greater | WB:WBVar00000510 | Pipe-separated entries represent independent evidence; comma-separated entries represent grouped evidence, e.g. two of three genes in a triply mutant organism
8 | Interacting_taxon_ID ::= NCBITaxon:[Taxon_ID] | | 0 or greater | NCBITaxon:5476 |
8 | Interacting_taxon_ID ::= ['NCBITaxon:'Taxon_ID] ('\|' \| ‘,’ 'NCBITaxon:'[Taxon_ID])* | | 0 or greater | NCBITaxon:5476 |
9 | Date ::= YYYY-MM-DD | | 1 | 2019-01-30 |
10 | Assigned_by ::= Prefix | | 1 or greater | MGI |
11 | Annotation_Extensions ::= [Extension_Conj] ('\|' Extension_Conj)* | | 0 or greater | BFO:0000066(GO:0005829) |
12 | Annotation_Properties ::= [Property_Value_Pair] ('\|' Property_Value_Pair)* | | 0 or greater | contributor-id=https://orcid.org/0000-0002-1478-7671 |

Taxon_ID ::= Digit+

The Taxon_ID should be a taxon identifier from the NCBI Taxonomy database.

Extension_Conj ::= [Relational_Expression] (',' Relational_Expression)*

Relational_Expression ::= Relation_ID '(' ID ')'

Relation_ID ::= ID

The Relation_ID may be from the Relations Ontology or from the set of GO relations, go_rel.

Property_Value_Pair ::= Property_Symbol '=' Property_Value
Expand Down