To support practical application and mapping
Document Information
| Document Title: | Guidelines for Best Practice to support Application and Mapping of Ontologies |
Brief Description: | These best practice guidelines are designed to check how suitable source ontologies are for mapping. It places emphasis on the application of ontologies in the Life Science industry to encourage best practice and to aid mapping of ontologies in a particular domain. This public resource was developed as part of the Pistoia Alliance Ontologies Mapping project. |
| Prepared by: | The Pistoia Alliance Ontologies Mapping Project team |
| Date: | 7th April 2016 |
| Version: | 1.2 |
Contents
1. Context and Purpose
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Many ontologies in the Disease, Phenotype and Experimental Investigation domains have textual definitions (vocabulary) for class terms which makes them more likely to bring unique value for application. A high proportion of quality textual definitions will facilitate interoperability through mapping the meaning (semantics) of equivalence in different ontologies.
3.13. Naming conventions
Naming conventions used by ontology providers tend to be a heterogeneous and inconsistent. This is because names emerge often in an ad hoc manner rather than through an agreed nomenclature. Of course there are exceptions which are much more mature and consistent, such as the HUGO Gene Nomenclature Committee which provides the authoritative source of human gene names (http://www.genenames.org). Another excellent example is Chemical Entities of Biological Entities (ChEBI) which started as a curated nomenclature for small molecules and has developed into a mature ontology in the OBO Foundry. The OBO principle wiki page, FP_012_naming_conventions (http://wiki.obofoundry.org/wiki/index.php/FP_012_naming_conventions) is under development and mostly mentions the publication entitled "Survey-based naming conventions for use in OBO Foundry ontology development” by Schober et al 2009 (http://www.biomedcentral.com/1471-2105/10/125). This guideline aligns with Malone et al 2016 Rule 5: Textual Definitions Should Be Written for Domain Experts.
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Positive and negative aspects of the above guidelines of best practice are listed in the Table below. The positive aspects are encouraged whereas the negative aspects can hinder application and mapping of ontologies and should to be avoided or minimised:-
| Guideline | Positive aspect | Negative aspect |
|---|---|---|
1.Format | Open standard | Non-standard |
| 2.URIs | Used and persistent | Not used and not persistent |
| 3.Versioning | Used with date | Not used and no date |
| 4.Documentation | High quality and coverage | Poor or absent |
| 5.Users | Evidence beyond provider | Poor or missing evidence |
| 6.Authority | Clearly defined | Unclear or missing |
| 7.Maintenance | Evidence of currency and sustainability | Poor or missing evidence |
| 8.License | Clearly defined terms and conditions | License terms can restrict use |
| 9.Content delineation | Clear | Unclear or no delineation |
| 10.Content coverage* | Acceptable | Inadequate or sparse or gaps |
| 11.Content quality* | Acceptable | Poor or inaccurate |
| 12.Textual definitions* | Acceptable | Insufficient or absent |
| 13.Naming conventions* | Acceptable | Insufficient or absent |
| 14.Relations | Consistent, clear model | Inconsistent |
| 15.Conserved URIs | Cross reference to source URIs | Missing source URIs |
*tested through relevant sampling
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to OBO principles and the 10 rules of Malone et al 2016
| Guideline | OBO Principle | 10 Rules of Malone et al 2016 |
|---|---|---|
1.Format | http:// |
| www.obofoundry.org/ |
| principles/fp-002-format.html | ||
| 2.URIs | http://wiki.obofoundry.org/wiki/index.php/FP_003_URIs | Rule 3: The Ontology Classes and Relationships Should Persist. |
| 3.Versioning | http://wiki.obofoundry.org/wiki/index.php/FP_004_versioning | Rule 8: Previous Versions Should Be Available |
| 4.Documentation | http://wiki.obofoundry.org/wiki/index.php/FP_008_documented |
| 5.Users | http://wiki.obofoundry.org/wiki/index.php/FP_009_users | Rule 6: The Ontology Should Be Developed by the Community but Not Incapacitated by It |
| 6.Authority | http://wiki.obofoundry.org/wiki/index.php/FP_011_locus_of_authority | Rule 6: The Ontology Should Be Developed by the Community but Not Incapacitated by It |
| 7.Maintenance | http://wiki.obofoundry.org/wiki/index.php/FP_016_maintenance | Rule 7: The Ontology Should Be under Active Development |
| 8.License | http://wiki.obofoundry.org/wiki/index.php/FP_001_open | Rule 9: Open Data Requires Open Ontologies |
| 9.Content delineation | http://wiki.obofoundry.org/wiki/index.php/FP_005_delineated_content | Rule 1: The Ontology Should Be about a Specific Domain of Knowledge |
| 10.Content coverage |
| Rule 2: The Ontology Should Reflect Current Understanding of Biological Systems | ||
| 11.Content quality |
| Rule 2: The Ontology Should Reflect Current Understanding of Biological Systems | ||
| 12.Textual definitions | http://wiki.obofoundry.org/wiki/index.php/FP_006_textual_definitions | Rule 4: Classes Should Contain Textual Definitions |
| 13.Naming conventions | http://wiki.obofoundry.org/wiki/index.php/FP_012_naming_conventions | Rule 5: Textual Definitions Should Be Written for Domain Experts |
| 14.Relations | http://wiki.obofoundry.org/wiki/index.php/FP_007_relations |
| 15.Conserved URIs |
6. References
- The Open Biological and Biomedical Ontologies (OBO) Foundry (http://www.obofoundry.org)
- NCBO BioPortal (http://bioportal.bioontology.org)
- "Survey-based naming conventions for use in OBO Foundry ontology development” by Schooner et al 2009 (http://www.biomedcentral.com/1471-2105/10/125)
- Arp, Smith and Spear: Building Ontologies with Basic Formal Ontology published by MIT Press, August 17, 2015
- Malone et al "Ten Simple Rules for Selecting a Bio-ontology" PLOS: Computational Biology 2016 DOI:10.1371/journal.pcbi 1004743.