mitsuhashi/togoid-config

Definition of link data for TogoID

TogoID config

Description of link data for TogoID.

Link data

Pair of database IDs in the tab separated value (TSV) format. The name of this file should be listed in the following config file.

DB1ID1	DB2IDx
DB1ID2	DB2IDy
DB1ID3	DB2IDz
 :

Config

Metadata for pair of databases and their relation.

# Source database (the 1st column of the link data file)
source:
  # Human readable label (intended to be used in a Web UI)
  label: KEGG Orthology
  # Category (should be a class defined in the TogoID ontology; TBD)
  type: Ortholog
  # Unique short name (intended to be used as a name space in RDF)
  # Recommended to use the prefix name defined at prefixcommons.org
  namespace: kegg.orthology
  # URI prefix (intended to be used as a prefix in RDF)
  prefix: http://identifiers.org/kegg.orthology/

# Target database (the 2nd column of the link data file)
target:
  label: Gene Ontology
  type: Function
  namespace: go
  prefix: http://purl.obolibrary.org/obo/

# Relation of the pair of database identifiers
link:
  # File name(s) of link data
  file: link.tsv
#  file:
#    - link.1.tsv
#    - link.2.tsv

  # Forward link (source to target)
  forward:
    label: functionally related to
    namespace: ro
    # Ontology URI which defines predicates
    prefix: http://purl.obolibrary.org/obo/
    # Selected predicate defined in the above ontology
    predicate: RO_0002328

  # Reverse link (optional; target to source)
  reverse:
    label: enabled by
    namespace: ro
    prefix: http://purl.obolibrary.org/obo/
    predicate: RO_0002333

# Metadata for updating link data
update:
  # How often the source data is updated
  frequency: Monthly
  # Update procedure of link data (can be a script name or a command like)
  method: curl http://rest.genome.jp/link/go/ko | cut -f 1,2 | perl -pe 's/ko://; s/go:/GO_/' > link.tsv

Recommended to use Dublin Core™ Collection Description Frequency Vocabulary DCFreq terms to specify the update frequency.

Usage

config-summary

To summarize all config settings:

% ruby bin/config-summary link/*/config.yaml > config-summary.tsv
% vd config-summary.tsv

To see the database update frequency:

% ruby bin/config-summary link/*/config.yaml | cut -f1,18

To see the database update method:

% ruby bin/config-summary link/*/config.yaml | cut -f1,19

togoid-config

To check the syntax of the config YAML file:

% ruby bin/togoid-config link/uniprot-hgnc/config.yaml

To update link data from the data source:

% ruby bin/togoid-config link/uniprot-hgnc/config.yaml update

To generate a RDF/Turtle file for the given link data:

% ruby bin/togoid-config link/uniprot-hgnc/config.yaml convert > uniprot-hgnc.ttl