Advancing the accuracy of open chemical information with CAS Common Chemistry

Presentation to ACS Spring in April 5-30, 2021 (Virtual)Science Inventory, CCTE products: https://cfpub.epa.gov/si/si_public_search_results.cfm?advSearch=true&showCriteria=2&keyword=CCTE&TIMSType=&TIMSSubTypeID=&epaNumber=&ombCat=Any&dateBeginPublishedPresented=07/01/2017&dateEndPublishedPresented=&dateBeginUpdated=&dateEndUpdated=&DEID=&personName=&personID=&role=Any&journalName=&journalID=&publisherName=&publisherID=&sortBy=pubDate&count=25</p

MOESM1 of XMetDB: an open access database for xenobiotic metabolism

Additional file 1. Example of exported SDF file from XMetDB

Key entities in CHEMINF ontology and their immediate superclasses.

<p>The key CHEMINF entities are chemical domain specialisations of more general terms in IAO and OBI. They are: chemically relevant format specification, algorithm, software module, chemical graph, and software execution.</p

The chemical graph representation of cyclohexane.

<p>The chemical graph illustrates the atoms and bonds within a chemical entity, with the exception of hydrogen atoms and their accompanying bonds, which are commonly left implicit since their presence can be deduced from the remainder of the skeleton of the molecule. The graph is illustrated both in 2D and in 3D with the accompanying connection table and coordinates.</p

Data transformation.

<p>A data transformation is an example of a parameterized software execution. A software execution is differentiated from a software method or module in that the software execution is a single process which has concrete parameter values as input. On the other hand, a software method or module may be executed over and over with many different parameters.</p

Lipinski query results.

<p>The diagram illustrates the Protégé query tab and the results of executing a Lipinski drug-likeness query on the generated CHEMINF knowledge base.</p

Textual and numeric data format specifications.

<p>An example of format specifications are those which constrain the format of a data item to be textual or numeric. In the case of a numeric format specification, only numeric digits are allowed in the data item. Format specifications are essential when designing robust software for complex research pipelines.</p

Algorithms and software implementations.

<p>Algorithms are differentiated in the ontology from the software which implements them. The same algorithm may, for example, be implemented in several different programming languages. The smallest unit of software which we identify is the software method. Methods have parameter data items as input and generate resulting data items as output. Software methods also may generate warning or error messages. Multiple software methods are grouped together into a software module. A software module may conform to an algorithm which has specified output a particular descriptor.</p

MOESM1 of PubChemRDF: towards the semantic annotation of PubChem compound and substance databases

Additional file 1. The supporting information for the paper entitled: PubChemRDF: towards the semantic annotation of PubChem compound and substance databases

Chemical descriptors.

<p>A chemical descriptor conforms to a data format specification. It is about a chemical entity (an example of which might be ‘caffeine’), and is a descriptor of a property of that chemical entity (such as its charge). The descriptor value is linked to the chemical entity in the ontology with the <i>has attribute</i> relation.</p