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Protocols

OWLTools specifications

Information


Unique identifier OMICS_29539
Name OWLTools
Alternative names OWL2LS, OWL2 Life Sciences
Software type Application/Script
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Programming languages Java, Javascript, Perl, R, Shell (Bash)
License BSD 3-clause “New” or “Revised” License
Computer skills Advanced
Version 0.3.0
Stability Stable
Maintained Yes

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Documentation


Additional information


https://github.com/owlcollab/owltools/wiki

OWLTools citations

 (9)
library_books

Disease Model Discovery from 3,328 Gene Knockouts by The International Mouse Phenotyping Consortium

2017
Nat Genet
PMCID: 5546242
PMID: 28650483
DOI: 10.1038/ng.3901

[…] uidance-applicants; PhenStat, http://goo.gl/tfbA5k; MGI, http://www.informatics.jax.org/; MGI downloads, ftp://ftp.informatics.jax.org/pub/reports/; Monarch Initiative, https://monarchinitiative.org; OWLtools, https://github.com/owlcollab/owltools […]

library_books

Single Copy Genes as Molecular Markers for Phylogenomic Studies in Seed Plants

2017
Genome Biol Evol
PMCID: 5414570
PMID: 28460034
DOI: 10.1093/gbe/evx070

[…] ed the A. thaliana annotation from TAIR (release 06/03/2016) and the P. pinaster annotation predicted by InterProScan (v5.15-54). GO terms for both species were mapped to GO slim plant by Map2Slim in OWLTools. […]

call_split

Modeling biochemical pathways in the gene ontology

2016
PMCID: 5009323
PMID: 27589964
DOI: 10.1093/database/baw126
call_split See protocol

[…] nload-ontology). The work described here used the core editor’s version of GO, gene_ontology_write.obo, and imported external ontologies. Ontologies can be converted between OBO and OWL formats using owltools (https://github.com/owlcollab/owltools). The OBO format was used for human readability during the manual quality checking and for work in OBO-Edit and the OWL format was used for work in Prot […]

library_books

Ontology application and use at the ENCODE DCC

2015
PMCID: 4360730
PMID: 25776021
DOI: 10.1093/database/bav010

[…] rresponding set of GO slim terms, a process called slimming, including the web-based AmiGO (http://amigo1.geneontology.org/cgi-bin/amigo/slimmer) and command-line owl tools (https://code.google.com/p/owltools/). However, a limitation of these tools is that they require a known set of annotations. To accommodate our use of multiple ontologies and slims, we chose to write our own code (https://githu […]

library_books

Standardized description of scientific evidence using the Evidence Ontology (ECO)

2014
PMCID: 4105709
PMID: 25052702
DOI: 10.1093/database/bau075

[…] gy as appropriate. Reasoning is performed to check term relationships and intra-ontology cross-product term validity. Releases are generated by the OBO Ontology Release Tool (http://code.google.com/p/owltools/wiki/Oor tIntro), and both OBO and OWL versions of the ontology are provided. The HermiT reasoner is run as part of the release cycle, to verify that the ontology is formally coherent, and to […]

library_books

A method for increasing expressivity of Gene Ontology annotations using a compositional approach

2014
BMC Bioinformatics
PMCID: 4039540
PMID: 24885854
DOI: 10.1186/1471-2105-15-155

[…] ns. RPH coordinated the writing of the paper. RPH, MAH, JAB, DPH, JL, RCL, CJM, KV-A and VW contributed to the writing of the paper. SJC is responsible for the development of AmiGO2. HD worked on the OWLTools code for folding/unfolding. All authors read and approved the final manuscript. […]

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