We evaluated the classification method on a gold standard derived from the PubMed Supplementary Concept annotations, achieving a micro-average F1-score of 85.9% for primary subtypes.
The parts of the MeSH tree associated with chemicals is composed of two parts, the 'Chemicals and Drugs' branch of the MeSH hierarchy and an independent set of supplementary concept records (denoted as MeSH substances).
CTD's chemical dictionary is a modified subset of descriptors from the "Chemicals and Drugs" category and Supplementary Concept Records from the U.S. National Library of Medicine NLM Medical Subject Headingsgs, a hierarchical vocabulary used to index PubMed articles containing > 100 000 chemicals.
One recent change for ontologies/vocabularies at RGD was the conversion from a MeSH (Medical Subject Headings -based disease vocabulary to a disease vocabulary based on a combination of MeSH terms ('C' branch and terms from supplementary concept data) and OMIM terms (Online Mendelian Inheritance in Man, http://www.omim.org, http://www.ncbi.nlm.nih.gov/omim).nih.gov/omim
Notes: [mp.=title, abstract, original title, name of substance word, subject heading word, keyword heading word, protocol supplementary concept word, rare disease supplementary concept word, unique identifier].
[mp = title, abstract, original title, name of substance word, subject heading word, protocol supplementary concept, rare disease supplementary concept, unique identifier] 9. or/1-8 10. randomized controlled trial.pt.pt
An example is the MeSH supplementary concept IUPAC from PMID 20128619 in the abstract set [21].
The document indexing was based on terms of the MeSH tree associated with chemicals (Chemicals and Drugs branch and supplementary concept records called MeSH substances).
It offers a different –a supplementary– set of standards".
[mp=protocol supplementary concept, rare disease supplementary concept, title, original title, abstract, name of substance word, subject heading word, unique identifier] 19.
