Bioi 7711 Team Project
We are going to try to produce working code that evaluates OBO ontologies using (primarily) natural language processing tools. The goal is to implement a few of the easier and fully automatable metrics proposed in our white paper. As the project progresses, relevant materials will be posted here. To start with, here are some useful background papers and web sites:- Documentation for the Gene Ontology
- OBO Ontologies available through the BioPortal (and a FAQ and web services for the BioPortal). [It seems as if some of the links on the web services part of the BioPortal are broken; here is a Junit test application that runs through the main web services and should be useful for getting started. Nick Griffith (ngriff @ stanford . edu) who is responsible for maintaining these has offered to help us.] A subset of these ontologies, called the OBO Foundry are intended to meet a set of principles that make them particularly useful. We will probably want to focus on these foundry ontologies.
- Our paper from last summer's ISMB which is a reasonable model for what we are trying to achieve (note that it was about annotation using the GO, not about the creation of the ontology itself). This paper from PSB 2006 describes some NLP-related methods applied to ontologies.
- Background papers on: Terms used for talking about ontologies (want to know what continuants or instances are?). The current (well, most recently published) state of the GO and a historical perspective. A reasonable example of the data description use case.
- Johnson, et al., paper from PSB '06 about lexical methods for detecting relationships among concepts in different ontologies (same as the one mentioned above).
- Bada and Hunter paper on making mappings between different ontologies.
- Barry Smith, et al., paper on circularity and comprehensibility in ontology terms and definitions.
References from Mike's talk on 11/6:
-
Desiderata:
- Cimino, J. J. (1998) Desiderata for controlled medical vocabularies in the twenty-first century. Methods Inf. Med. 37(4-5), 394-403.
- Burgun, A. (2006) Desiderata for domain reference ontologies in biomedicine. J. Biomed. Inform. 39(3), 307-313.
-
Ontology-evaluation techniques:
- Gomez-Perez, A. (2001) Evaluation of Ontologies. Internat. J. of Intell. Systems 16, 391-409.
- Brank, J., Grobelnik, M., and Mladenic, D. (2005) A Survey of Ontology Evaluation Techniques. Proc. 8th Internat. multi-conference Inf. Soc. IS, 166-169.
-
Others
- Noy, N. F., Guha, R., and Musen, M. A. (2005) User ratings of ontologies: Who will rate the raters? AAAI 2005 Spring Symp. on Knowledge Collection from Volunteer Contributors.
- Groot, P., van Harmelen, F., and ten Teije, A. (2000) Torture Tests: A Quantitative Analysis for the Robustness of Knowledge-Based Systems. Knowledge Acquisition, Modeling and Management, LNAI 1319, 403-418. Berlin:Springer-Verlag.
Infrastructure
- Sample code for interfacing with the OBO-Edit API: OboEdit_Util.java (Note: the OBO-Edit libraries are needed to run this code. They can be downloaded here: http://oboedit.org/)
- A project twiki will be available sometime next week.
- SQL*Plus will be made available on compbio sometime soon.
