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Readme.v3.0b
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Biocaster Ontology v3.0b README
Version 3.0b is still very much a work in progress but is released as a pre-beta in the hope that it will be useful and to solicit feedback and corrections. The known issues we are currently working on are listed below.
More information on the methods and sources used to construct the ontology can be found in:
[1] Collier, N., Matsuda-Goodwin, R., McCrae, J., Doan, S., Kawazoe, A., Conway, M., Kawtrakul, A., Takeuchi, K. and Dien, D. (2010), .An ontology-driven system for detecting global health events., Proc. 23rd International Conference on Computational Linguistics (COLING), Beijing, China, August 23-27.
[2] Collier, N., Kawazoe, A., Jin, L., Shigematsu, M., Dien, D. Barrero, R., Takeuchi , K.and Kawtrakul, A. (2007), .A multilingual ontology for infectious disease surveillance: rationale, design and challenges., Language Resources and Evaluation, Elsevier, DOI: 10.1007/s10579-007-9019-7.
Issues
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a) Translation verification
Newly added terms for several languages still need to be verified. These include: Arabic, French, Indonesian, Korean, Malay, Spanish, Vietnamese and Chinese.
b) Species identifiers for symptoms
Human symptoms are still being renamed as "symtom (human)".
c) Single species specific diseases
These are currently exceptions to the "disease (species)" naming convention as there is no ambiguity.
d) Terms requiring translation
A few terms still require translation, e.g. Difficulty swallowing (human); these are under consideration.
e) Animal disease symptoms
We are now working to expand the symptoms for animal diseases in line with veterinary sources.
f) External links
Several require verifying and are now likely stale, including MeSH (e.g. Marek Disease which has a dead link) and Pathport.
g) SUMO links
Concepts from SUMO need to be properly linked to their SUMO identifiers.
Change Notes
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Version 3.0b:
(1) All disease and symptom terms specific to their groups now have specific suffix labels (e.g., Tularemia (Lagomorph), Rabies (Human)). However, those symptom and disease terms that now have suffix labels still need to have a translated suffix for each language. For example, Athlete foot (Human) still does not have (Human) added to the translated "Athlete foot" in all languages.
(2) Each disease now has corresponding symptoms specific to each animal group (e.g., Tularemia (Lagomorph) has Chills (Lagomorph), Fever (Lagomorph), Lethargy (Lagomorph).
(3) Almost all symptom terms now belong to the specific syndrome(s) (e.g., Conjnctivitis (Bovine) indicates Constitutional Syndrome (Veterinary)).