Finding a common standard for the representation of bibliographic information
(PLEASE EDIT AND UPDATE THIS WIKI PAGE TO MAKE IT MORE COMPLETE)
Many of the Semantic Web ontologies in the domain of HCLS contain constructs for the representation of bibliographic information and references to database entries. Unfortunately, it seems that most of them came up with their own solutions, which naturally leads to a lot of confusion, redundancy and missing interoperability.
Here is a list of ontologies that have impemented their own constructs for bibliographic information and their strategies for re-using existing ontologies or metadata standards:
Ontology |
makes use of existing standard |
BioPAX |
no |
Birnlex |
imports Dublin Core and parts of FOAF; (to the developers of Birnlex: please add more information about this) |
bio-zen plus |
integrates FOAF and Dublin Core; some additional classes were added, several unnecessary classes were removed from FOAF; FOAF and Dublin Core were modified to conform to OWL DL |
Neurocommons annotations |
pubmed ids |
Senselab / NeuronDB |
no |
SWAN |
no |
kind-of! This is part of the TDWG LSID Vocabularies. It is still some what volatile. This ontology is based on a combination of suggestions from TaxMLit, TaxonX and a draft 0.95 of TCS which was, in turn based on Rich Pyle's Taxonomer data model which was inspired by Endnote 7. It is planned to synonymise as many of the properties in this vocabulary to widely used vocabularies as possible e.g. MARC etc. |
|
Makes use of slightly modifierd version of Dublin Core and FOAF. Also uses BibTex properties, but with own namespace (not the one from 'bibtex in OWL') |
|
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Ontologies and metadata standards that could (should?) be re-used
(ordered based on significance)
Bibliographic Data Ontology created by Tom Gruber, represented in KIF, based on Frames
Dublin Core Element Set (Schema information / download) -- the most important standard, pretty basic, only properties. Needs to be slightly modified before it can be integrated into valid OWL DL ontologies.
FOAF (Schema information / download) -- by far the most widespread Semantic Web ontology to date. Includes classes like "Document" or "Image". Needs a lot of pruning before integration into a pure life science ontology (many silly entities, unnecessary mapping to Wordnet need to be removed). Needs to be modified before it can be integrated into valid OWL DL ontologies.
SwetoDblp Integrates FOAF and Dublin Core, there is already a large amount of data available (export of the DBLP database).
Annotea (Schema information / download) -- seems like it has not been updated in a long time. Could not locate a schema. Seems to make use of FOAF and Dublin Core.
- (add something here)
The Bibliographic Ontology Specification Group (Google groups website) might be of interest.
Standard URIs for bibliographic entities
Besides the issues with differing ontologies, there are also widel differing URI schemes used for bibliographic entities, e.g.:
- info URI scheme
- LSIDs (e.g. for Pubmed entries)
- ISBN URI scheme
- (add something here)
Please be aware that the discussion about URI schemes is independent from the discussion about standard ontologies, and probably of a lower priority at the moment.