What exactly are the UMLS and SNOMED-CT vocabularies used by cTAKES?

Question

Very new to cTAKES and looking through the docs, curious about what exactly the UMLS and SNOMEDCT "vocabularies" are. The user installation docs don't really seem to tell and simply applying for the UMLS license and the language around the UMLS Metathesaurus does not really divulge much more about the structure of the data being accessed. Eg. is it some online API service? Is it some files that come with the cTAKES download that can only be unlocked with a valid UMLS password that is checked against an online DB?

Answer 1

Info on what the UMLS Metathesaurus and SNOMEDCT are can be found here (https://www.nlm.nih.gov/research/umls/knowledge_sources/metathesaurus/index.html) and here (https://www.ncbi.nlm.nih.gov/books/NBK9676/, specifically https://www.ncbi.nlm.nih.gov/books/NBK9684/):

The Metathesaurus is a very large, multi-purpose, and multi-lingual [relational?] vocabulary database that contains information about biomedical and health related concepts, their various names, and the relationships among them. Designed for use by system developers...

...The Metathesaurus contains concepts, concept names, and other attributes from more than 100 terminologies, classifications, and thesauri, some in multiple editions.

While I'm not sure how exactly cTAKES implements its use of the UMLS Metathesaurus (anyone who knows could please enlighten), I assume that it is accessing some API for a relational database based on the UMLS credentials you need to add to the example scripts that come with the cTAKES download (see https://cwiki.apache.org/confluence/display/CTAKES/cTAKES+4.0+User+Install+Guide#cTAKES4.0UserInstallGuide-(Recommended)AddUMLSaccessrights).

...You may select from two relational formats: the Rich Release Format (RRF), introduced in 2004, and the Original Release Format (ORF).

(I think) this is what is used to power the UIMA analysis engines used to process text in cTAKES

UIMA is an architecture in which basic building blocks called Analysis Engines (AEs) are composed in order to analyze a document [...] How Annotators represent and share their results is an important part of the UIMA architecture. To enable composition and reuse, UIMA defines a Common Analysis Structure (CAS) precisely for these purposes. The CAS is an object-based container that manages and stores typed objects having properties and values, https://www.ibm.com/developerworks/data/downloads/uima/#How-does-it-work