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EFO Tools
Below a table summarising EFO supporting tools:
Java
| Ontology Common API Tasks
(OntoCAT) |
Download |
| OntoCAT
provides high level abstraction for interacting with ontology
resources including local ontology files in standard OWL and
OBO formats (via OWL
API) and public ontology repositories: EBI Ontology Lookup
Service (OLS) and NCBO BioPortal. Each resource is wrapped
behind easy to learn Java, Bioconductor/R and REST web service
commands enabling reuse and integration of ontology software
efforts despite variation in technologies. Developed together
with Morris Swertz's group at the
Groningen Bioinformatics Centre. |
| Ontology Diff (bubastis) |
Web Version
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|
| An ontology change tool which is able to
analyse two ontologies (typically two versions of the same
ontology) to highlight logical changes which have occurred and
to present these changes in more or less detail, as required. |
| Zooma |
Download |
| ZOOMA is an application for discovering
optimal ontology mappings, designed to automatically map text
values to ontology terms. |
| Tab2OWLclass |
Download
|
| Java tool for importing classes into an
already existing OWL file. The script uses the OWL-API to read
in a tab delimited file of class details and create OWL classes
from these rows, adding them to an existing ontology. |
| EFO Web Site (dr
manhattan) |
Download
|
| Java EE implementation providing basic
functionality for an ontology web front-end and serving stable
HTTP URIs for ontology concepts according to Linked Data
principles. |
| EFO query expansion |
Download
|
| Source code for the ArrayExpress
Archive Web Interface , which uses EFO and Lucene indexing to
expand user queries, e.g. search for cancer and return
also all experiments containing adenocarcinoma in their
descriptions, as well as all the synonyms for cancer
children terms. |
Perl
| Mappings Tools |
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|
| Perl package providing fuzzy concept
recognition based on a list of terms and any target ontology.
Lexical matching is implemented using n-grams and supports text
transpositions. It is also possible to align one ontology to
another (synonyms included). Supported formats are OWL, OBO,
MeSH ASCII, OMIM, and tab-delimtied text files. |
| OWL-Simple |
Download
|
| This package contains a set of Perl modules
for parsing OWL ontologies and a simple converter to OBO
format. Available via CPAN. |
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