PDB GOA README
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1.  Contents
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1.  Contents
2.  Introduction
3.  File format
4.  Contacts
5.  Copyright Notice

2.  Introduction
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This file has been generated from a collaboration between the InterPro, PDB and
GOA teams. Manual and electronic GO annotations are provided in this
file from two sources:

1. where an InterPro entry matches a PDB chain, annotations supplied by the
InterPro2GO electronic method are assigned to the chain identifier (for further
details on this method see:
http://www.geneontology.org/cgi-bin/references.cgi#GO_REF:0000002)

2. PDB chains are additionally supplied with manual and electronic GO annotations
(excluding InterPro2GO) where a PDB chain maps with at least 90% identity to a
UniProtKB accession (more specifically with the UniProtKB's CHAIN feature),
whereupon manual and electronic annotations are supplied to the PDB chain identifier
from the matching UniProtKB accession.

GOA (GO Annotation) is a project run by the European Bioinformatics
Institute that aims to provide assignments of gene products to the Gene
Ontology (GO) resource.  The goal of the Gene Ontology Consortium is to
produce a dynamic controlled vocabulary that can be applied to all eukaryotes,
even while knowledge of gene and protein roles in cells is still accumulating and
changing. For futher information on GOA please refer to our web site at:
http://www.ebi.ac.uk/GOA

3.  File format
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goa_pdb.gaf

Since we deal with proteins rather than genes, the semantics of some
fields in our files may be slightly different to other gene association files.

1.  DB
    Database from which entry has been taken.
    Example: PDB

2.  DB_Object_ID
    A unique identifier in the DB for the item being annotated.
    Here: PDB ID and chain ID of the PDB entry.
    Example: 2EKB_A

3.  DB_Object_Symbol
    Here: PDB ID and chain ID of the PDB entry.
    Example:EKB_A

4.  Qualifiers
    This column is used for flags that modify the interpretation of an annotation.
    This field may be equal to: NOT, colocalizes_with, contributes_to,
    NOT|contributes_to, NOT|colocalizes_with
    Example: NOT

5.  GO Identifier
    The GO identifier for the term attributed to the DB_Object_ID.
    Example: GO:0005625

6.  DB:Reference
    A single reference cited to support an annotation.
    Where an annotation cannot reference a paper, this field will contain
    a GO_REF identifier. See section 8 and
    http://www.geneontology.org/doc/GO.references
    for an explanation of the reference types used.
    Examples: PMID:9058808
              DOI:10.1046/j.1469-8137.2001.00150.x
              GO_REF:0000002
              GO_REF:0000020
              GO_REF:0000004
              GO_REF:0000003
              GO_REF:0000019
              GO_REF:0000023
              GO_REF:0000024

7.  Evidence
    One of either EXP, IMP, IC, IGI, IPI, ISS, IDA, IEP, IEA, TAS, NAS,
    NR, ND or RCA.
    Example: TAS

8.  With
    An additional identifier to support annotations using certain
    evidence codes (including IEA, IPI, IGI, IC and ISS evidences).
    Examples: UniProtKB:O00341
              InterPro:IPROO1878
	      Ensembl:ENSG00000136141
              GO:0000001
              EC:3.1.22.1

9.  Aspect
    One of the three ontologies: P (biological process), F (molecular function)
    or C (cellular component).
    Example: P

10. DB_Object_Name
    Always empty

11. Synonym
    Always empty.

12. DB_Object_Type
    What kind of entity is being annotated.
    Always: protein_structue

13. Taxon_ID
    Identifier for the species being annotated.
    Example: taxon:9606

14. Date
    The date of last annotation update in the format 'YYYYMMDD' eg: 20030228

15. Assigned_By
    Attribute describing the source of the annotation.  One of
    either UniProtKB, AgBase, BHF-UCL, DictyBase, Ensembl, FB, GDB, GeneDB,
    GR (Gramene), HGNC, LIFEdb, MGI, Reactome, RGD, Roslin Institute,
    SGD, TAIR, TIGR, ZFIN, IntAct, PINC (Proteome Inc.) or WormBase.
    Example: UniProtKB

16. Annotation_Extension (N.B. Until annotation practices are finalised,
    this column will remain empty). This column is intended to contain cross references
    to other ontologies/databases that can be used to qualify or enhance the annotation.
    The cross-reference is prefaced by an appropriate GO relationship; references to multiple
    ontologies
    can be entered.
    Example: part_of(CL:0000084)
	     occurs_in(GO:0009536)
	     has_input(CHEBI:15422)
	     has_output(CHEBI:16761)
	     has_participant(UniProtKB:Q08722)
	     part_of(CL:0000017)|part_of(MA:0000415)

17. Gene_Product_Form_ID
    This column will remain empty in this file as this column is intended to describe
    specific products of the gene/canonical protein described in column 2 (DB_Object_ID).



4. Contacts
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Please direct any questions to goa@ebi.ac.uk.  We welcome any feedback.

5. Copyright Notice
--------------------

GOA - UniProt GO Annotation Project
Copyright 2016 (C) The European Bioinformatics Institute.
This README and the accompanying databases may be copied and
redistributed freely, without advance permission, provided that this
copyright statement is reproduced with each copy.

$Date: 2017/09/19 14:12:36 $