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Home of the Genomic Feature and Variation Ontology (GFVO)

Home Page: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4435477/

Shell 4.97% Ruby 95.03%

ontology genomics genomic-data-science gff3 gtf gvf vcf

ontologies's Introduction

BioInterchange Ontologies

Bioinformatics related ontologies. Especially for generating RDF content using BioInterchange.

Genomic Feature and Variation Ontology (GFVO)

An ontology for describing genomic features and variants; in particular the contents of GFF3, GTF, GVF and VCF files.

https://raw.github.com/BioInterchange/Ontologies/master/gfvo.xml

Build Instructions

Build instructions are intended for collaborators and enthusiasts who would like contributing to the BioInterchange ontologies. The ontologies can be edited using Protege, but a few post-processing steps are necessary to remove additional information that Protege inserts on its own.

Post-Protege-Cleanup

Saving an ontology with Protege will introduce explicit class definitions and individuals for external URIs. These have to be removed, so that only BioInterchange URIs are described by the ontologies. A script has been provided that takes care of this, and additionally, increments the patch level version number of the ontologies.

For example, the following commands can be used to create a new cleaned version of the GFVO ontology:

<gfvo.xml scripts/cleanse.rb > gfvo.tmp
mv gfvo.tmp gfvo.xml

Generating GFVO for BioPortal

Due to technical limitations of BioPortal, GFVO in BioPortal cannot import other ontologies or contain SIO class- or property-equivalences. If ontologies are imported and equivalences kept, then BioPortal reports from summary statistics and the class browser shows thousands of classes that are not part of GFVO itself.

Removal of OWL imports and class- and property-equivalences:

grep -v '<owl:imports ' gfvo.xml | grep -v '<owl:equivalentProperty ' | grep -v '<owl:equivalentClass ' > gfvo_bioportal.xml

Generating Statistics

Summary statistics about classes and properties can be output in human-readable and HTML via:

./scripts/stats.rb < gfvo.xml

Generating new GO Abbreviation Collection Link-Outs

A regular expression of valid URIs as defined in the Gene Ontology Abbreviation Collection can be automatically generated using the following command:

./scripts/go_xref2xsd_pattern.rb

On Mac OS X, the generated regular expression can be copied into the clipboard for subsequent pasting using the pbcopy command:

./scripts/go_xref2xsd_pattern.rb | pbcopy

Deprecated Ontologies

The following ontologies were prototypes that eventually merged into the Genomic Feature and Variation Ontology (GFVO).

Generic Feature Format Version 3 Ontology (GFF3O)

An ontology for describing GFF3 file contents.

https://raw.github.com/BioInterchange/Ontologies/master/gff3o.xml

Genome Variation Format Version 1 Ontology (GVF1O)

An ontology for describing GVF file contents.

https://raw.github.com/BioInterchange/Ontologies/master/gvf1o.xml

ontologies's People

Contributors

Stargazers

Watchers

Forkers

tfuji micheldumontier bioinformaticsarchive sphkan

ontologies's Issues

"sequence_variant" correctly represented in class diagram?

The object property "sequence_variant" (http://www.biointerchange.org/gvf1o#GVF1_0042) might be wrongly labeled in the class diagram (not publicly available).

Comment about heritage needs to be updated for "Quality"

"Maternal"/"Paternal" were renamed to "Maternal Heritage"/"Paternal Heritage". Might occur in various other comments too.

ontology_term ObjectProperty range

The range of this property is a giant UnionOf class expression, none of the elements of which are ontology terms.

For example:

http://amigo.geneontology.org/cgi-bin/amigo/term-details.cgi?term=GO:

Is not an ontology term. It's the prefix for a URL that when appendex with a GO number will resolve to a page about the ontology term.

Domain/Range of "attributes" correct?

The "attributes" object property (http://www.biointerchange.org/gvf1o#GVF1_0152) has unassigned domain/range.

FAIRsharing query - GFVO

Dear GFVO Developers,

I’m contacting you on behalf of FAIRsharing[1], the online registry of scientific data standards, databases and policies. Our aim is to make your resource as visible as possible to as large an audience as possible.

We have a FAIRsharing record for your resource[2]. To ensure our information is as correct and up to date as possible, would you or someone from your team quickly scan the record[2] and ‘claim’ it? (To claim, see link [3] below.)

Claiming a record as either a group or an individual also gives you the opportunity to make changes to the record yourself, allowing you complete control over how your resource is displayed in FAIRsharing. In addition, if you claim a record(s) as an individual, you can link the record to your ORCID.

FAIRsharing is about making your resource discoverable to a variety of users, such as journals and publishers, researchers and service providers, research and infrastructure projects and programmes, as well as curators, librarians, funders and other policy makers and data scientists[4]. A contact is essential should they have any questions about your resource.

Thank you and best wishes,
Allyson

[1] https://fairsharing.org, https://doi.org/10.1038/s41587-019-0080-8
[2] https://doi.org/10.25504/FAIRsharing.vbejb6
[3] https://fairsharing.org/own/standard/claim/bsg-s000959
[4] https://fairsharing.org/communities

Provide sample RDF

It's not really clear how to use many of the classes and properties. It would help to provide sample data in RDF. I'm aware this is possible using the API etc but I think it would help if there were some blessed examples provided.

Typo for FALDO Import

The import line for faldo should be changed from

<owl:imports rdf:resource="http://www.biointerchange.org/faldo.owl"/>

<owl:imports rdf:resource="http://biohackathon.org/resource/faldo.ttl"/>

I've been trying to open the gfvo.xml file in Protege, and FALDO is always improperly imported and assigned to TEMP. Looking at the code, it is because the wrong URL was assigned for the FALDO import. The URI itself is correct though.