Archive for the ‘UMLS’ Category

Cleaning UMLS data and Loading into Graph

Monday, March 3rd, 2014

Cleaning UMLS data and Loading into Graph by Sujit Pal.

From the post:

The little UMLS ontology I am building needs to support two basic features in its user interface – findability and navigability. I now have a reasonable solution for the findability part, and I am planning to use Neo4j (a graph database) for the navigability part.

Just to get you interested in the post, here is the outcome:

The server exposes a Web Admin client (similar to the Solr Admin client) at port 7474 (http://localhost:7474/webadmin/). The dashboard shows 2,880,385 nodes, 3,375,083 properties, 58,021,093 relationships and 653 relationship types, which matches with what we put in. (emphasis added)

Enjoy!

Understanding UMLS

Sunday, February 23rd, 2014

Understanding UMLS by Sujit Pal.

From the post:

I’ve been looking at Unified Medical Language System (UMLS) data this last week. The medical taxonomy we use at work is partly populated from UMLS, so I am familiar with the data, but only after it has been processed by our Informatics team. The reason I was looking at it is because I am trying to understand Apache cTakes, an open source NLP pipeline for the medical domain, which uses UMLS as one of its inputs.

UMLS is provided by the National Library of Medicine (NLM), and consists of 3 major parts: the Metathesaurus, consisting of over 1M medical concepts, a Semantic Network to categorize concepts by semantic type, and a Specialist Lexicon containing data to help do NLP on medical text. In addition, I also downloaded the RxNorm database that contains drug/medication information. I found that the biggest challenge was accessing the data, so I will describe that here, and point you to other web resources for the data descriptions.

Before getting the data, you have to sign up for a license with UMLS Terminology Services (UTS) – this is a manual process and can take a few days over email (I did this couple of years ago so details are hazy). UMLS data is distributed as .nlm files which can (as far as I can tell) be opened and expanded only by the Metamorphosis (mmsys) downloader, available on the UMLS download page. You need to run the following sequence of steps to capture the UMLS data into a local MySQL database. You can use other databases as well, but you would have to do a bit more work.

….

The table and column names are quite cryptic and the relationships are not evident from the tables. You will need to refer to the data dictionaries for each system to understand it before you do anything interesting with the data. Here are the links to the online references that describe the tables and their relationships for each system better than I can.

I have only captured the highlights from Sujit’s post so see his post for additional details.

There has been no small amount of time and effort invested in UMLS. Than names are cryptic and relationships not specified is more typical than any other state of data.

Take the opportunity to learn about UMLS and to ponder what solutions you would offer.

UMLS-SKOS

Sunday, October 31st, 2010

UMLS-SKOS

Abstract:

SKOS is a Semantic Web framework for representing thesauri, classification schemes, subject heading systems, controlled vocabularies, and taxonomies. It enables novel ways of representing terminological knowledge and its linkage with domain knowledge in unambiguous, reusable, and encapsulated fashion within computer applications. According to the National Library of Medicine, the UMLS Knowledge Source (UMLS-KS) integrates and distributes key terminology, classification and coding standards, and associated resources to promote creation of more effective and interoperable biomedical information systems and services “that behave as if they ‘understand’ the meaning of the language of biomedicine and health”. However the current information representation model utilized by UMLS-KS itself is not conducive to computer programs effectively retrieving and automatically and unambiguously interpreting the ‘meaning’ of the biomedical terms and concepts and their relationships.

In this presentation we propose using Simple Knowledge Organization System (SKOS) as an alternative to represent the body of knowledge incorporated within the UMLS-KS within the framework of the Semantic Web technologies. We also introduce our conceptualization of a transformation algorithm to produce an SKOS representation of the UMLS-KS that integrates UMLS-Semantic Network, the UMLS-Metathesaurus complete with all its source vocabularies as a unified body of knowledge along with appropriate information to trace or segregate information based on provenance and governance information. Our proposal and method is based on the idea that formal and explicit representation of any body of knowledge enables its unambiguous, and precise interpretation by automated computer programs. The consequences of such undertaking would be at least three fold: 1) ability to automatically check inconsistencies and errors within a large and complex body of knowledge, 2) automated information interpretation, integration, and discovery, and 3) better information sharing, repurposing and reusing (adoption), and extending the knowledgebase within a distributed and collaborative community of researchers. We submit that UMLS-KS is no exception to this and may benefit from all those advantages if represented fully using a formal representation language. Using SKOS in combination with the transformation algorithm introduced in this presentation are our first steps in that direction. We explain our conceptualization of the algorithms, problems we encountered and how we addressed them with a brief gap analysis to outline the road ahead of us. At the end we also present several use cases from our laboratories at the School of Health information Sciences utilizing this artifact.

WebEx Recording Presentation

Slides

The slides are good but you will need to watch the presentation to give them context.

My only caution concerns:

Our proposal and method is based on the idea that formal and explicit representation of any body of knowledge enables its unambiguous, and precise interpretation by automated computer programs.

I don’t doubt that our computers can return “unambiguous, and precise interpretation[s]” but that isn’t the same thing as “correct” interpretations.

The UMLS Metathesaurus: representing different views of biomedical concepts

Wednesday, October 27th, 2010

The UMLS Metathesaurus: representing different views of biomedical concepts

Abstract

The UMLS Metathesaurus is a compilation of names, relationships, and associated information from a variety of biomedical naming systems representing different views of biomedical practice or research. The Metathesaurus is organized by meaning, and the fundamental unit in the Metathesaurus is the concept. Differing names for a biomedical meaning are linked in a single Metathesaurus concept. Extensive additional information describing semantic characteristics, occurrence in machine-readable information sources, and how concepts co-occur in these sources is also provided, enabling a greater comprehension of the concept in its various contexts. The Metathesaurus is not a standardized vocabulary; it is a tool for maximizing the usefulness of existing vocabularies. It serves as a knowledge source for developers of biomedical information applications and as a powerful resource for biomedical information specialists.

Bull Med Libr Assoc. 1993 Apr;81(2):217-22.
Schuyler PL, Hole WT, Tuttle MS, Sherertz DD.
Medical Subject Headings Section, National Library of Medicine, Bethesda, MD 20894.

Questions:

  1. Did you notice the date on the citation?
  2. Map this article to the Topic Maps Data Model (3-5 pages, no citations)
  3. Where does the Topic Maps Data Model differ from this article? (3-5 pages, no citations)
  4. If concept = proxy, what concepts (subjects) don’t have proxies in the Metathesaurus?
  5. On what basis are “biomedical meanings” mapped to a single Metathesaurus “concept?” Describe in general but illustrate with at least five (5) examples

The Neighborhood Auditing Tool – Update

Tuesday, October 26th, 2010

The Neighborhood Auditing Tool for the UMLS and its Source Terminologies is a presentation mentioned here several days ago.

If you missed it, go to: http://bioontology.org/neighborhood-audiiting-tool for the slides and WEBEX recording.

Pay close attention to:

The clear emphasis on getting user feedback during the design of the auditing interface.

The “neighborhood” concept he introduces has direct application to XML editing.

Find the “right” way to present parent/child/sibling controls to users and you would have a killer XML application.

Questions:

  1. Slides 8 – 9. Other than saying this is an error (true enough), on what basis is that judgment made?
  2. Slides 18 – 20. Read the references (slide 20) on neighborhoods. Pick another domain, what aspects of neighborhoods are relevant? (3-5 pages, with citations)
  3. Slides 21 – 22. How do your neighborhood graphs compare to those here?
  4. Slides 23 – 46. Short summary of the features of NAT and no citation evaluation. Or, use NAT as basis for development of interface for another domain. (project)
  5. Slides 49 – 55. Visualizations for use and checking. Compare to current literature on visualization of vocabularies/ontologies. (project)
  6. Slides 56 – 58. Snomed browsing. Report on current status. (3-5 pages, citations)
  7. Slices 57 – 73. Work on neighborhoods and extents. To what extent is a “small intersection type” a sub-graph and research on sub-graphs applicable? Any number of issues and questions can be gleaned from this section. (project)