GFF3 is a tab-delimited, ontology-aware format of genomic features. It should be beneficial to represent such genomic features in RDF so that we can exchange data and make queries with SW technologies.
Participants
- Erick Antezana
- Alberto Labarga
- Yu Lin
- Hideya KAWAJI
- Venkata Satagopam
- Jerven Bolleman
- Mitsuteru Nakao
- ...
Scope
...
Mapping GFF2RDF (proposal)
The following table is in a very inmature state...
| GFF Element | RDF (XML) | Description |
| Column 1: "seqid" | <gff:seqid rdf:about="#ctg123"> | ? |
| Column 2: "source" | <gff:source>1000</gff:source> | ? |
| Column 3: "type" | <gff:type rdf:about="#SO:0000704"> | <rdfs:SubClassOf rdf:resource="#SO:0000704" /> | This is constrained to be either: (a) a term from the "lite" sequence ontology, SOFA; or (b) a SOFA accession number. It must map to a rdfs:subclassof (lin's proposal) |
| Column 4: "start" | <gff:start>1000</gff:start> | ? |
| Column 5: "end" | <gff:stop>9000</gff:stop> | ? |
| Column 6: "score" | <gff:score>5.8e-42</gff:score> | ? |
| Column 7: "strand" | <gff:strand>+</gff:strand> | ? |
| Column 8: "phase" | <gff:phase>.</gff:phase> | ? |
| Column 9: "attributes" | <gff:attributes><rdf:Description>...</rdf:Description></gff:attributes> | ? |
Attribute Mapping (proposal)
A list of feature attributes in the format tag=value. Multiple tag=value pairs are separated by semicolons. URL escaping rules are used for tags or values containing the following characters: ",=;". Spaces are allowed in this field, but tabs must be replaced with the ? URL escape.
| Attribute tags | RDF (XML) | Description |
| Column 1: "ID" | ||
| Column 2: "Name" | ||
| Column 3: "Alias" | ||
| Column 4: "Parent" | ||
| Column 5: "Target" | ||
| Column 6: "Gap" | ||
| Column 7: "Derives_from" | ||
| Column 8: "Note" | ||
| Column 9: "Dbxref" | ||
| Column 10: "Ontology_term" |
Tools
- Chris Mungall's code
- Tool for BioPython?
- Tool for BioRuby
- Tool for Perl
Discussion
- application to general genomic features (BED, etc)?
- Genomic coordinate system (0-based / 1-based)
- Dasty?
- Attributes is more important for describing an object.
Expected milestones
- Mapping GGF2RDF (by Q1?)
- Tools (in PERL, Python and Ruby) implementing such translation
- Sample RDF data into a triple store (e.g. OpenVirtuoso?)
- Sample SPARQL queries
- Divulgation (poster? or article?)
