Journal: PLoS ONE

Article Title: A Unique Transformation from Ordinary Differential Equations to Reaction Networks

doi: 10.1371/journal.pone.0014284

Figure Lengend Snippet: The incorrect structure of the corresponding SBML models (93 and 94) of the BioModels database can be automatically fixed by going back to the differential equations and extracting the unique structure fulfilling our three conditions. It then correctly includes the reversibility of reactions (1), (2), (3), (6), etc. highlighted in red, and absent from the BioModels database version.

Article Snippet: The XPPAUT.ode file (BIOMD151.ode) and the resulting structured SBML file (BIOMD151_new.xml) can be found at http://contraintes.inria.fr/~soliman/ode2pn_data/ together with the biomodels version (BIOMD0000000151.xml), which actually contains more errors than found by , mostly concerning parameter names that are quite error-prone when hand-translated from ODEs to SBML.

Techniques:

Journal: PLoS ONE

Article Title: A Unique Transformation from Ordinary Differential Equations to Reaction Networks

doi: 10.1371/journal.pone.0014284

Figure Lengend Snippet: The 68 ODEs actually allow the extraction of a unique model fulfilling the three established conditions. It not only correctly reflects the structure described in the article, but also avoids the typos introduced in the hand-written model 151 of the BioModels database; hand-typing an SBML model for that many ODEs with numerous parameters is definitely error-prone.

Article Snippet: The XPPAUT.ode file (BIOMD151.ode) and the resulting structured SBML file (BIOMD151_new.xml) can be found at http://contraintes.inria.fr/~soliman/ode2pn_data/ together with the biomodels version (BIOMD0000000151.xml), which actually contains more errors than found by , mostly concerning parameter names that are quite error-prone when hand-translated from ODEs to SBML.

Techniques: Extraction

Journal: AMIA Annual Symposium Proceedings

Article Title: Supporting Ontology-based Keyword Search over Medical Databases

doi:

Figure Lengend Snippet: Summary of the different methods for storing an ontology in a database.

Article Snippet: Original XML , ORG (vers, dat). The original NCI Thesaurus XML file (Apelon schema) is stored in the dat column, in one row of the ORG table. , Use the SQL/XML function XMLTable to extract the hyponym links and use recursive SQL to traverse those links. , Just insert the new NCI Thesaurus XML file. No preprocessing required..

Techniques: Full Display Name, Extraction

Journal: AMIA Annual Symposium Proceedings

Article Title: Supporting Ontology-based Keyword Search over Medical Databases

doi:

Figure Lengend Snippet: Fragment of the original XML format for the NCI Thesaurus and corresponding queries.

Article Snippet: Original XML , ORG (vers, dat). The original NCI Thesaurus XML file (Apelon schema) is stored in the dat column, in one row of the ORG table. , Use the SQL/XML function XMLTable to extract the hyponym links and use recursive SQL to traverse those links. , Just insert the new NCI Thesaurus XML file. No preprocessing required..

Techniques: