View source for Annotation Association File Format

==Overview==
Collaborating databases and projects provide the POC project a tab delimited file, known informally as a " association file". This file carries links between database objects and PO terms. The database object may represent one of gene, transcript, protein, protein_structure, complex, germplasm (stock/cultivar), mutant, QTL, etc. Columns in the file are described below. Here is a [http://brebiou.cshl.edu/viewcvs/*checkout*/Poc/associations/po_anatomy_gene_oryza_gramene.assoc sample file] containing association from Gramene database.

==File Name==

'''po_aspect_objecttype_organism_organization.assoc'''<br />

'''aspect:''' ''growth/anatomy/development''.<br />
'''objecttype:''' ''gene/mutant/germplasm/qtl'' etc.<br />
'''organism:''' is always GENUS e.g. ''arabidopsis/oryza/zea''.<br />
'''organization:''' the isntitute/project which is contributing the association files.<br />

For example:<br />
''po_anatomy_gene_arabidopsis_tair.assoc''<br />
''po_growth_gene_arabidopsis_tair.assoc''<br />
''po_anatomy_gene_oryza_gramene.assoc''<br />
''po_growth_gene_oryza_gramene.assoc''<br />

==File Format==

The flat file format comprises 16 tab-delimited fields (see also a further example containing several annotations). Make sure the column order is strictly followed.

* denotes required fields:


{| width="80%" border="1" cellspacing="3" cellpadding="4" align="center"
|- align="left" valign="middle"
| Column
| Content
| Example
|- align="left" valign="middle"
| 1. *
| DB
| GR
|- align="left" valign="middle"
| 2. *
| DB_Object_ID
| GR:0060905
|- align="left" valign="middle"
| 3. *
| DB_Object_Symbol
| lrd10
|- align="left" valign="middle"
| 4.
| Qualifier
|- align="left" valign="middle"
| 5. *
| PO ID
| PO:0007014
|- align="left" valign="middle"
| 6. *
| DB:Reference(|DB:Reference)
| GR_ref:5655|PMID:2676709
|- align="left" valign="middle"
| 7. *
| Evidence
| IMP
|- align="left" valign="middle"
| 8.
| With (or) From
|- align="left" valign="middle"
| 9. *
| Aspect
| G
|- align="left" valign="middle"
| 10.
| DB_Object_Name
| lesion resembling disease-10
|- align="left" valign="middle"
| 11.
| DB_Object_Synonym(|Synonym)
| spl4|bl5|spotted leaf-4
|- align="left" valign="middle"
| 12.*
| DB_Object_Type
| gene
|- align="left" valign="middle"
| 13.*
| taxon(|taxon)
| taxon:4527
|- align="left" valign="middle"
| 14.*
| Date
| 20050303
|- align="left" valign="middle"
| 15.*
| Assigned_by
| GR
|- align="left" valign="middle"
| 16.
| Annotation_extension
| part_of PO:0028002
|}

Additional information on can be found at the GO page for the [http://www.geneontology.org/GO.format.gaf-2_0.shtml GAF.20 format].

==Description of the content==

===1. DB===
*The database contributing the association file.
*One of the values in the table of database abbreviations. [Database abbreviations explanation]
*This field is mandatory, cardinality 1

===2. DB_Object_ID===
*A unique identifier in DB for the item being annotated.
*This field is mandatory, cardinality 1.

===3. DB_Object_Symbol===
*A (unique and valid) symbol to which DB_Object_ID is matched.
*Can use ORF name for otherwise unnamed gene or protein.
*If gene products are annotated, can use gene product symbol if available, or many gene product annotation entries can share a gene symbol.
*This field is mandatory, cardinality 1

===4. Qualifier===
*Flags that modify the interpretation of an annotation.
*One (or more) of NOT, contributes_to, colocalizes_with.
*This field is not mandatory; cardinality 0, 1, >1; for cardinality >1 use a pipe to separate entries (e.g. NOT|contributes_to).

===5. POid===
*The PO identifier for the term attributed to the DB_Object_ID.
*This field is mandatory, cardinality 1.

===6. DB:Reference===
*The unique identifier appropriate to DB for the authority for the attribution of the POid to the DB_Object_ID. This may be a literature reference or a database record. The syntax is DB:accession_number..
*Note that only one reference can be cited on a single line. If a reference has identifiers in more than one database, multiple identifiers can be included on a single line. For example, if the reference is a published paper that has a PubMed ID, we strongly recommend that the PubMed ID be included, as well as an identifier within a model organism database.
*This field is mandatory, cardinality 1, >1; for cardinality >1 use a pipe to separate entries (e.g. GR:8789|PMID:2676709).

===7. Evidence===
*One of IMP, IGI, IPI, IAGP, ISS, IDA, IEP, IEA, TAS, NAS, ND, IC, RCA.
*This field is mandatory, cardinality 1.

===8. With (or) From===
*One of:
**DB:gene_symbol
**DB:gene_symbol[allele_symbol]
**DB:gene_id
**DB:protein_name
**DB:sequence_id
**GO:GO_id
*This field is not mandatory (except in the case of IC evidence code), cardinality 0, 1, >1
*Note: This field is used to hold an additional identifier for annotations using certain evidence codes (IC, IEA, IGI, IPI, ISS). Cardinality = 0 is not recommended, but is permitted because cases can be found in literature where no database identifier can be found (e.g. physical interaction or sequence similarity to a protein, but no ID provided). Annotations where evidence is IGI, IPI, or ISS and 'with' cardinality = 0 should link to an explanation of why there is no entry in 'with.' Cardinality may be >1 for any of the evidence codes that use 'with'; for IPI and IGI cardinality >1 has a special meaning (see evidence documentation for more information). For cardinality >1 use a pipe to separate entries (e.g. TAIR:Atg111111|TAIR:Atg222222).
*Note that a gene/locus ID may be used in the 'with' column for a IPI annotation, or for an ISS annotation based on amino acid sequence or protein structure similarity, if the database does not have identifiers for individual gene products.
*'PO:PO_id' is used only when the evidence code is 'IC', and refers to the PO term(s) used as the basis of a curator inference. In these cases the entry in the 'DB:Reference' column will be that used to assign the PO term(s) from which the inference is made. This field is mandatory for evidence code IC.
*The ID is usually an identifier for an individual entry in a database (such as a sequence ID, gene ID, PO ID, etc.). Identifiers from the Center for Biological Sequence Analysis (CBS), however, represent tools used to find homology or sequence similarity; these identifiers can be used in the 'with' column for ISS annotations.

===9. Aspect===
*Either '''A''' (plant structure) or '''G''' (growth stage and development stage)
*This field is mandatory; cardinality 1

===10. DB_Object_Name===
*Name of the object. e.g. gene or gene product
*This field is not mandatory, cardinality 0, 1 [white space allowed]

===11. Synonym===
*Any aliases. e.g. Gene_symbol [or other text]
*This field is not mandatory, cardinality 0, 1, >1 [white space allowed]

===12. DB_Object_Type===
*What kind of thing is being annotated
*One of gene, transcript, protein, protein_structure, complex, germplasm (stock/cultivar), mutant, QTL etc.
*This field is mandatory, cardinality 1

===13. Taxon===
*What kind of thing is being annotated
*One of gene, transcript, protein, protein_structure, complex, germplasm (stock/cultivar), mutant, QTL etc.
*This field is mandatory, cardinality 1

===14. Date===
*Date on which the annotation was made; format is YYYYMMDD
*This field is mandatory, cardinality 1

===15. Assigned_by===
*The database which made the annotation
*One of the values in the table of database abbreviations. [http://plantontology.org/docs/dbxref/PO_DBXref.txt Database abbreviations explanation]
*Used for tracking the source of an individual annotation.
*Default value is value entered in column 1 (DB).
*Value will differ from column 1 for any that is made by one database and incorporated into another.
*This field is mandatory, cardinality 1

===16. Annotation_extension===
'''NOTE: Usage specifications for column 16 for the PO is under development. Check with curators before using this column'''

*Contains cross references to a PO term that can be used to qualify or enhance the annotation. The cross-reference is prefaced by an appropriate PO relationship (part_of, participates_in for PO terms). 
*One or more of: relation PO:id 
*Example 1: If a gene product is localized to the leaf tip of a vascular leaf, the PO ID (column 5) would be leaf tip (PO:0025142), and the annotation extension column would contain a cross-reference to part_of vascular leaf (PO:0009025).
*Example 2: If a gene product is localized in a leaf during senesence, the PO ID (column 5) would be leaf (PO:0009025), and the annotation extension column would contain a cross-reference to participates_in leaf senescence stage (PO:0001054).
*Example 3: 
*This field is not mandatory, cardinality 0, 1, >1; for cardinality >1 use a pipe to separate entries (e.g., part_of PO:0009025|participates_in PO:0001054).
*See additional information and discussion on the [[PO Annotation Extensions (column 16)]] page.

===Note===
Several fields contain database cross-reference (dbxrefs) in the format dbname:dbaccession. The fields are: POid (where dbname is always PO), DB:Reference, With, Taxon (where dbname is always taxon), Annotation extension. For PO ids, do not repeat the 'PO:' prefix (i.e. always use PO:0000000, not PO:PO:00000000)

[[Category:SOP]]