PERSONNEL

Jim Mork photo

Jim Mork, MS

Applied Clinical Informatics Branch
Computer Scientist

Contact Information
Building 38A - Lister Hill Center, 7S704
301.827.4996
jmork@mail.nih.gov


Expertise and Research Interests:

Mr. Mork is currently the lead developer and technical project lead for the Medical Text Indexer (MTI) project. The MTI project is a multi-divisional team developing the MTI program to assist indexers and catalogers in assigning keywords to over 600,000 biomedical related articles and books each year. Mr. Mork’s research interests include information retrieval, natural language processing, and extracting information from biomedical literature.

Mr. Mork received his BS in Computer Science from Central Michigan University in 1984 and his MS in Computer Science from The Johns Hopkins University in 1988.

Mr. Mork’s previous experiences at Rapid Systems Solutions, Inc., Century Computing, Inc., VisionQuest Consulting, Inc., and previous Government employment have covered most aspects of Computer Science and Project Leadership. His main focus has been on Rapid Application Prototyping.

Honors and Awards:

  • 2016 - Frank B. Rogers Award recipient.
  • 2015 -  Library Operations Choice Awards Certificate of Appreciation for completing the study and policy change proposals to add preliminary MeSH indexing to In-Process citations to improve PubMed retrieval.
  • 2015 - Quality Step Increase for Sustained High Quality Work Performance.
  • 2014 - Recognition and Appreciation of Special Achievement for normalization of section headers within the MEDLINE structured abstracts.
  • 2013 - Library Operations Choice Awards Certificate of Appreciation for implementing an automated indexing process for the NLM Technical Bulletin.
  • 2011 - Exceptional Service by a Contractor for Medical Text Indexer First Line Prototype development.
  • 2011 – Special Act or Service Award for MTI as First Line Indexer Development and Pilot Production Project.
  • 2009 – Exceptional Service by a Contractor for Medical Text Indexer Catalog support.
  • 2008 – Special Act or Service Award for Medical Text Indexer Catalog support.
  • 2008 – Letter of Appreciation for Office of Director NIH Biennial Report support.

Publications:

Lu C, Payne A, Mork J. Proper filter usage to retrieve multiwords from the MEDLINE n-gram set: Reply to the Turki et al commentary "Enhancing filter-based parenthetic abbreviation extraction methods". Journal of the American Medical Informatics Association, Volume 28, Issue 3, March 2021, Page 670, https://doi.org/10.1093/jamia/ocaa313.

Lu CJ, Payne A, Mork JG. The Unified Medical Language System SPECIALIST Lexicon and Lexical Tools: Development and applications. J Am Med Inform Assoc. 2020 May 29;27(10):1600-1605. doi: 10.1093/jamia/ocaa056.

Lu CJ, Payne A, Mork JG. Enhanced Features in the SPECIALIST Lexicon - Antonyms. AMIA 2020 Virtual Annual Symposium, November 14-18, 2020.

Savery M, Rogers W, Pillai M, Mork JG, Demner-Fushman D. Chemical Entity Recognition for MEDLINE Indexing. AMIA 2020 Virtual Informatics Summit, 2020.

Rae A, Savery M, Mork JG, Demner-Fushman D. A High Recall Classifier for Selecting Articles for MEDLINE Indexing. AMIA Fall Symposium, 2019.

Savery M, Huston M, Mork JG, Printseva O, Rae A, Schmidt S, Demner-Fushman D. Evaluation of System for Selective Indexing Classification. AMIA Fall Symposium, 2019.

Mork JG, Aronson A, Demner-Fushman D. 12 years on - Is the NLM medical text indexer still useful and relevant?. J Biomed Semantics. 2017 Feb 23;8(1):8. doi: 10.1186/s13326-017-0113-5.

Demner-Fushman D, Mork JG. NLM Medical Text Indexer. Technical Report to the LHNCBC Board of Scientific Counselors April 2016

Demner-Fushman D, Mork JG. Extracting Characteristics of the Study Subjects from Full-Text Articles. AMIA Annu Symp Proc. 2015 Nov 5;2015:484-91. eCollection 2015.

Read KB, Sheehan JR, Huerta MF, Knecht LS, Mork JG, Humphreys BL. Sizing the Problem of Improving Discovery and Access to NIH-Funded Data: A Preliminary Study. PLoS One. 2015 Jul 24;10(7):e0132735. doi: 10.1371/journal.pone.0132735. eCollection 2015.

Cho D, Mork JG, Aronson A, Demner-Fushman D, Schmidt S, Ozga D, Pash J, Kilbourne J. MeSH on demand: an easy way to identify relevant MeSH terms and related articles from text [Poster]. National Cancer Institute (NCI) Symposium "RNA Biology 2015".

Jimeno Yepes AJ, Plaza L, Carrillo-de-Albornoz J, Mork JG, Aronson A. Feature engineering for MEDLINE citation categorization with MeSH. BMC Bioinformatics. 2015 Apr 8;16:113. doi: 10.1186/s12859-015-0539-7.

Ripple AM, Mork JG, Schmidt SC, Thomson H, Knecht LS. Performance Comparison of MEDLINE Structured Abstract to Unstructured Abstracts [Poster]. 2014 NIH Research Festival.

Mork JG, Demner-Fushman D, Schmidt SC, Aronson A. Vocabulary Density Method for Personalized Indexing of MEDLINE Journals [Poster]. 2014 AMIA Symposium.

Mork JG, Demner-Fushman D, Schmidt SC, Aronson A. Recent Enhancements to the NLM Medical Text Indexer. . BioASQ 2014.

Demner-Fushman D, Mork JG, Aronson AR. Mining MEDLINE for problems associated with vitamin D. AMIA Annu Symp Proc. 2013 Nov 16;2013:300-8. eCollection 2013.

Yepes AJ, Mork JG, Demner-Fushman D, Aronson AR. Comparison and combination of several MeSH indexing approaches. AMIA Annu Symp Proc. 2013 Nov 16;2013:709-18. eCollection 2013.

Jimeno-Yepes AJ, Plaza L, Mork JG, Aronson AR, Díaz A. MeSH indexing based on automatically generated summaries. BMC Bioinformatics. 2013 Jun 26;14:208. doi: 10.1186/1471-2105-14-208.

Jimeno-Yepes AJ, Sticco JC, Mork JG, Aronson AR. GeneRIF indexing: sentence selection based on machine learning. BMC Bioinformatics. 2013 May 31;14:171. doi: 10.1186/1471-2105-14-171.

Jimeno Yepes A, Mork JG, Aronson A. Using the argumentative structure of scientific literature to improve information access [Poster]. BioNLP 2013.

Mork JG, Jimeno Yepes A, Aronson A. The NLM Medical Text Indexer System for Indexing Biomedical Literature. . BioASQ 2013.

Jimeno Yepes AJ, Mork JG, Aronson A. Identifying PublicationTypes Using Machine Learning. BioASQ Workshop 2013.

Jimeno-Yepes A, Mork J, Demner-Fushman D, Aronson AR. A one-size-fits-all indexing method does not exist: automatic selection based on meta-learning. JCSE, vol. 6, no. 2, pp.151-160, 2012.

Aronson AR, Mork J, Lang FM, Rogers W, Jimeno-Yepes A, Sticco JC. The NLM Indexing Initiative: Current Status and Role in Improving Access to Biomedical Information. April 2012 Technical Report to the LHNCBC Board of Scientific Counselors.

Jimeno-Yepes A, Wilkowski B, Mork JG, Demner-Fushman D, Aronson AR. MeSH indexing: machine learning and lessons learned. ACM SIGHIT International Health Informatics Symposium, Miami, FL, USA, 2012.

Jimeno-Yepes A, Mork JG, Wilkowski B, Demner-Fushman D, Aronson AR. MEDLINE MeSH indexing: lessons learned from machine learning and future directions. Proc IHI 2012, 737-742.

Jimeno-Yepes A, Mork J, Demner-Fushman D, Aronson AR. Automatic algorithm selection for MeSH Heading indexing based on meta-learning. . International Symposium on Languages in Biology and Medicine, Singapore, December, 2011.

Ripple AM, Mork JG, Humphreys BL, Knecht LS. A retrospective cohort study of structured abstracts in MEDLINE, 1992-2006. J Med Libr Assoc. 2011 Apr;99(2):160-3. doi: 10.3163/1536-5050.99.2.009.

Mork J, Peters L, Jimeno-Yepes A, Aronson AR, Bodenreider O. MetaMap in the CALBC Workshop II. CALBC Workshop II, March 2011.

Jimeno-Yepes A, Wilkowski B, Mork J, van Lenten E, Demner-Fushman D, Aronson AR. A bottom-up approach to MEDLINE indexing recommendations. AMIA Annu Symp Proc. 2011;2011:1583-92. Epub 2011 Oct 22.

Mork JG, Aronson AR. The Medical Text Indexer (MTI) system for indexing biomedical literature. book chapter submitted to monograph Indexing Specialities: Medicine. Edited by L. Pilar Wyman. Medford, NJ: Information Today, Inc., in association with the American Society of Indexers, Phoenix, AZ. 2010.

Demner-Fushman D, Mork JG, Shooshan SE, Aronson AR. UMLS content views appropriate for NLP processing of the biomedical literature vs. clinical text. J Biomed Inform. 2010 Aug;43(4):587-94. doi: 10.1016/j.jbi.2010.02.005. Epub 2010 Feb 10.

Névéol A, Mork JG, Aronson AR. Comment on 'MeSH-up: effective MeSH text classification for improved document retrieval'. Bioinformatics. 2009 Oct 15;25(20):2770-1; author reply 2772. doi: 10.1093/bioinformatics/btp483. Epub 2009 Aug 11.

Névéol A, Shooshan SE, Humphrey SM, Mork JG, Aronson AR. A recent advance in the automatic indexing of the biomedical literature. J Biomed Inform. 2009 Oct;42(5):814-23. doi: 10.1016/j.jbi.2008.12.007. Epub 2008 Dec 30.

Aronson AR, Mork JG, Neveol A, Shooshan SE, Demner-Fushman D. Methodology for Creating UMLS Content Views Appropriate for Biomedical Natural Language Processing. AMIA Annu Symp Proc. 2008 Nov 6:21-5

Aronson AR, Mork JG, Lang FM, Rogers WJ, Neveol A. NLM Medical Text Indexer: A Tool for Automatic and Assisted Indexing. April 2008 Technical Report to the LHNCBC Board of Scientific Counselors.

Demner-Fushman D, Humphrey SM, Ide NC, Loane RF, Mork J, Ruch P, Ruiz ME, Smith LH, Wilbur WJ, Aronson AR. Combining Resources to Find Answers to Biomedical Questions. Proc TREC 2007, 205-14

Névéol A, Mork JG, Aronson AR. Automatic indexing of specialized documents: using generic vs. domain-specific document representations. Proc 2007 Workshop BioNL'07, 183-92.

Névéol A, Shooshan SE, Mork JG, Aronson AR. Fine-grained indexing of the biomedical literature: MeSH subheading attachment for a MEDLINE indexing tool. AMIA Annu Symp Proc. 2007 Oct 11:553-7.

Aronson AR, Bodenreider O, Demner-Fushman D, Fung KW, Lee VK, Mork JG, Névéol A, Peters L, Rogers WJ. From indexing the biomedical literature to coding clinical text: experience with MTI and machine learning approaches. Proc 2007 Workshop BioNL'07, June 2007, pp. 105-112, Prague, Czech Republic.

Névéol A, Mork JG, Aronson AR, Darmoni SJ. Evaluation of French and English MeSH indexing systems with a parallel corpus. AMIA Annu Symp Proc. 2005:565-9.

Kim GR, Aronson AR, Mork JG, Cohen BA, Lehmann CU. Application of a Medical Text Indexer to an Online Dermatology Atlas. MedInfo. 2004 Sept.;2004.

Aronson AR, Demner-Fushman D, Humphrey SM, Ide NC, Kim W, Liu H, Loane RF, Mork JG, Smith LH, Tanabe LK, Wilbur WJ, Xie N. Knowledge-intensive and statistical approaches to the retrieval and annotation of genomics MEDLINE citations. The Thirteenth Text Retrieval Conference (TREC 2004). 2004:503-11.

Libbus B, Kilicoglu H, Rindflesch TC, Mork JG, Aronson AR. Using Natural Languge Processing, Locus Link, and the Gene Ontology to Compare OMIM to MEDLINE. Proceedings of the HLT-NAACL Workshop on Linking the Biological Literature, Ontologies and Databases: Tools for Users. 2004;:69-76.

Aronson AR, Mork JG, Gay CW, Humphrey SM, Rogers W. The NLM Indexing Initiative's Medical Text Indexer. Stud Health Technol Inform. 2004;107(Pt 1):268-72.

Mitchell JA, Aronson AR, Mork JG, Folk LC, Humphrey SM, Ward JM. Gene Indexing: Characterization and Analysis of NLM's GeneRIFs. AMIA Annu Symp Proc. 2003:460-4.

Kayaalp M, Aronson AR, Humphrey SM, Ide NC, Tanabe LK, Smith LH, Demner-Fushman D, Loane RF, Mork JG, Bodenreider O. Methods for accurate retrieval of MEDLINE citations in functional genomics. The Twelfth Text Retrieval Conference (TREC 2003). 2003:441-50.

Srinivasan S, Rindflesch TC, Hole WT, Aronson AR, Mork JG. Finding UMLS Metathesaurus Concepts in MEDLINE. Proc AMIA Symp. 2002:727-31.

Weeber M, Mork JG, Aronson AR. Developing a Test Collection for Biomedical Word Sense Disambiguation. Proc AMIA Symp. 2001:746-50.

Weeber M, Klein H, Aronson AR, Mork JG, de Jong-van den Berg LT, Vos R. Text-Based Discovery in Biomedicine: The Architecture of the DAD-System. AMIA Annu Symp Proc. 2000 ;():903-7.

Aronson AR, Bodenreider O, Chang HF, Humphrey SM, Mork JG, Nelson SJ, Rindflesch TC, Wilbur WJ. The NLM Indexing Initiative. Proc AMIA Symp. 2000:17-21.