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Journal articles on the topic 'UML2'

Author: Grafiati

Published: 4 June 2021

Last updated: 1 February 2022

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1

Louati, Aymen, and Kamel Barkaoui. "Formal Verification of UML2 Timing Diagrams based on Time Petri Nets." International Journal of Information Systems in the Service Sector 8, no. 2 (April 2016): 87–97. http://dx.doi.org/10.4018/ijisss.2016040107.

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Unified Modeling Language (UML) is using in the design notation in industry and academia projects. Interesting by the critical Real-Time System verification, it is important to ensure its dependability in order to avoid eventual errors. In this paper, the authors aim to extend the UML diagrams by adding a formal verification stage. They tackle with the UML2 timing diagram (TD), as interaction diagram in order to describe the system's behavior in temporal way. For that, the authors give a formal description for TD using Time Petri Nets (TPN). Then, they propose a formal verification by means of Romeo Model Checker. In particular, they show how to formulate quantitative properties using TCTL (timed computation tree logic). In addition, the authors show how they can derive the TCTL formulae from Object Constraint Language-Real Time (OCLRT) constraints. Finally, they illustrate the proposed approach through a real case study.

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Duddy, Keith. "UML2 must enable a family of languages." Communications of the ACM 45, no. 11 (November 2002): 73–75. http://dx.doi.org/10.1145/581571.581596.

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Boufenara, Sabine, Kamel Barkaoui, Faiza Belala, and Hanifa Boucheneb. "Transactional Petri nets: a semantic framework for UML2 activities." International Journal of Critical Computer-Based Systems 5, no. 3/4 (2014): 241. http://dx.doi.org/10.1504/ijccbs.2014.064663.

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Thomas, Dave. "UML - Unified or Universal Modeling Language? UML2, OCL, MOF, EDOC - The Emperor Has Too Many Clothes." Journal of Object Technology 2, no. 1 (2003): 7. http://dx.doi.org/10.5381/jot.2003.2.1.c1.

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5

Bennama, Miloud, and Thouraya Bouabana Tebibel. "Validation environment of UML2 IOD based on hierarchical coloured Petri nets." International Journal of Computer Applications in Technology 47, no. 2/3 (2013): 227. http://dx.doi.org/10.1504/ijcat.2013.054372.

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6

Arpinen, Tero, Erno Salminen, Timo D. Hämäläinen, and Marko Hännikäinen. "Performance Evaluation of UML2-Modeled Embedded Streaming Applications with System-Level Simulation." EURASIP Journal on Embedded Systems 2009 (2009): 1–16. http://dx.doi.org/10.1155/2009/826296.

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7

Elallaoui, Meryem, Khalid Nafil, Raja Touahni, and Rochdi Messoussi. "Automated Model Driven Testing Using AndroMDA and UML2 Testing Profile in Scrum Process." Procedia Computer Science 83 (2016): 221–28. http://dx.doi.org/10.1016/j.procs.2016.04.119.

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8

Buerth, Christoph, Filip Kovacic, Janpeter Stock, Marius Terfrüchte, Susanne Wilhelm, Karl-Erich Jaeger, Michael Feldbrügge, Kerstin Schipper, Joachim F. Ernst, and Denis Tielker. "Uml2 is a novel CalB-type lipase of Ustilago maydis with phospholipase A activity." Applied Microbiology and Biotechnology 98, no. 11 (January 28, 2014): 4963–73. http://dx.doi.org/10.1007/s00253-013-5493-6.

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9

Kreku, Jari, Mika Hoppari, Tuomo Kestilä, Yang Qu, Juha-Pekka Soininen, Per Andersson, and Kari Tiensyrjä. "Combining UML2 Application and SystemC Platform Modelling for Performance Evaluation of Real-Time Embedded Systems." EURASIP Journal on Embedded Systems 2008, no. 1 (2008): 712329. http://dx.doi.org/10.1155/2008/712329.

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10

Laibinis, Linas, Elena Troubitsyna, and Sari Leppänen. "Service-Oriented Development of Fault Tolerant Communicating Systems." International Journal of Embedded and Real-Time Communication Systems 1, no. 2 (April 2010): 61–85. http://dx.doi.org/10.4018/jertcs.2010040104.

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Telecommunication systems must have a high degree of availability, that is, a high probability of correct and timely provision of requested services. To achieve this, correctness of software for such systems should be ensured. Application of formal methods helps increase confidence in building correct software. However, to be used in practice, formal methods should be well integrated into existing development process. In this paper, the authors propose a formal model-driven approach to development of communicating systems. The authors formalize and extend the Lyra approach—a top-down service-oriented method for development of communicating systems. Lyra is based on transformation and decomposition of models expressed in UML2. The authors formalize Lyra in the B Method by proposing a set of formal specification and refinement patterns reflecting the essential models and transformations of the Lyra phases. Moreover, this paper extends Lyra to integrate reasoning about fault tolerance in the entire development flow.

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Báscones, Elena, Juan Imperial, Tomás Ruiz-Argüeso, and Jose Manuel Palacios. "Generation of New Hydrogen-RecyclingRhizobiaceae Strains by Introduction of a Novelhup Minitransposon." Applied and Environmental Microbiology 66, no. 10 (October 1, 2000): 4292–99. http://dx.doi.org/10.1128/aem.66.10.4292-4299.2000.

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ABSTRACT Hydrogen evolution by nitrogenase is a source of inefficiency for the nitrogen fixation process by the Rhizobium-legume symbiosis. To develop a strategy to generate rhizobial strains with H2-recycling ability, we have constructed a Tn5derivative minitransposon (TnHB100) that contains the ca. 18-kb H2 uptake (hup) gene cluster fromRhizobium leguminosarum bv. viciae UPM791. Bacteroids from TnHB100-containing strains of R. leguminosarum bv. viciae PRE, Bradyrhizobium japonicum, R. etli, and Mesorhizobium loti expressed high levels of hydrogenase activity that resulted in full recycling of the hydrogen evolved by nitrogenase in nodules. Efficient processing of the hydrogenase large subunit (HupL) in these strains was shown by immunoblot analysis of bacteroid extracts. In contrast, Sinorhizobium meliloti,M. ciceri, and R. leguminosarum bv. viciae UML2 strains showed poor expression of the hup system that resulted in H2-evolving nodules. For the latter group of strains, no immunoreactive material was detected in bacteroid extracts using anti-HupL antiserum, suggesting a low level of transcription ofhup genes or HupL instability. A general procedure for the characterization of the minitransposon insertion site and removal of antibiotic resistance gene included in TnHB100 has been developed and used to generate engineered strains suitable for field release.

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12

Saripalle, Rishi Kanth. "UMLS Semantic Network as a UML Metamodel for Improving Biomedical Ontology and Application Modeling." International Journal of Healthcare Information Systems and Informatics 10, no. 2 (April 2015): 34–56. http://dx.doi.org/10.4018/ijhisi.2015040103.

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In the domain of biomedical and health informatics, ontologies are widely used to capture knowledge ranging from bioinformatics such as gene, protein, protein interactions, etc. to clinical/healthcare informatics knowledge such as diseases, symptoms, treatment, medication, etc. Currently, one medical knowledge source that encapsulates a broad spectrum of medical knowledge is the Unified Medical Language System (UMLS), which can be defined as a compendium of diverse medical ontological standards. The primary components of the UMLS are: Semantic Network (UMLS-SN) – designed by interconnecting well-defined semantic types with semantic relationships, and Metathesaurus (UMLS-META) – the base of UMLS system that is comprised of millions of medical concepts from diverse medical standards. However, within the biomedical and health informatics community, the concepts of software engineering and domain modeling (using meta-models such as ERD, UML, and XML) are very successful in designing and implementing biomedical/health domain application models. In the current status, the UMLS-SN is primarily employed for classification of medical concepts in UMLS-META, but UMLS-SN knowledge can't be viewed or employed as a modeling framework for designing ontological models and is restricted to the UMLS environment. Thus, the impact of the biomedical semantics captured by UMLS-SN might be minimal in medical facilities, research and healthcare organizations that are highly influenced by software engineering, meta-models and domain model-based practices. In order fill this gap, the authors propose a meta-modeling framework for UMLS-SN based on the UML Profile (built using UML meta-model) that will result in a customized domain specific meta-model. This specialized meta-model that encapsulates the medical knowledge semantics of UMLS-SN can then be employed for designing ontological models or relevant healthcare application models and simultaneously be coherent with software meta-models and domain modeling practices.

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PARVEEN, HEENA, NEHA BISHT, and LAKSHMI TEWARI. "OPTIMIZATION AND BIOCHEMICAL CHARACTERIZATION OF THERMO-ALKALOTOLERANT CELLULASE ENZYME FROM ASPERGILLUS TERREUS PPCF." Cellulose Chemistry and Technology 54, no. 9-10 (November 11, 2020): 967–76. http://dx.doi.org/10.35812/cellulosechemtechnol.2020.54.93.

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The aim of this study was to boost the production rate of a novel thermo-alkalotolerant cellulase (FPase) enzyme from the fungal isolate Aspergillus terreus PPCF. Initially, the extracellular FPase activity was 0.166 ± 0.03 UmL-1 in the culture filtrate, which further increased up to 0.91 ± 0.13 UmL-1 under optimized conditions (3% w/v wheat bran and 0.5% w/v ammonium sulfate). Through response surface methodology, the FPase activity was enhanced to 10.78 UmL1 under the cumulative effect of different factors. The zymogram analysis revealed only one activity band, with the molecular weight of ~110 KDa. The optimum pH was 7.0, but the enzyme was stable in a pH range of 4-10. The optimum temperature was 50 °C, but the stability range of the enzyme was 30-90 °C. The maximum effect of Mg2+ was observed on the FPase enzyme. The findings of the present study demonstrate the thermo- and alkalotolerance of the obtained cellulase enzyme, which will be beneficial to the biofuel and other industries.

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14

Kushnick, Louis. "Racism, the National Health Service, and the Health of Black People." International Journal of Health Services 18, no. 3 (July 1988): 457–70. http://dx.doi.org/10.2190/leuw-x7vw-q2kd-uml9.

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Racism has been and is central to an understanding of the health of black people in Britain. Black people have played and are playing a central role in the National Health Service (NHS). Their role is, however, shaped by racism. Their experiences as consumers of the NHS are also shaped by racism—in terms of their treatment for both physical and mental health problems. In addition, their specific health problems such as sickle cell anemia have not received the attention they deserve. The NHS has become part of the internal control system of the British racist immigration system. The cuts in the NHS, and in other areas of the welfare state, since 1979 have created the conditions for increasing racial conflict on the one hand and for interracial class-based resistance on the other.

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15

NAKAJIMA, N. "Application of Rheology to Polymer Processing." Journal of Elastomers and Plastics 32, no. 1 (January 1, 2000): 46–59. http://dx.doi.org/10.1106/3dn0-um52-d5l2-26a7.

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16

Gopalakrishnan, B., R. W. Plummer, and N. M. Alkadi. "Analysis of Energy Conservation Opportunities in Glass Manufacturing Facilities." Energy Engineering 98, no. 6 (October 1, 2001): 27–49. http://dx.doi.org/10.1092/umw2-n6a6-jmtp-6axk.

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17

Amos, Liz, David Anderson, Stacy Brody, Anna Ripple, and Betsy L. Humphreys. "UMLS users and uses: a current overview." Journal of the American Medical Informatics Association 27, no. 10 (July 19, 2020): 1606–11. http://dx.doi.org/10.1093/jamia/ocaa084.

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Abstract The US National Library of Medicine regularly collects summary data on direct use of Unified Medical Language System (UMLS) resources. The summary data sources include UMLS user registration data, required annual reports submitted by registered users, and statistics on downloads and application programming interface calls. In 2019, the National Library of Medicine analyzed the summary data on 2018 UMLS use. The library also conducted a scoping review of the literature to provide additional intelligence about the research uses of UMLS as input to a planned 2020 review of UMLS production methods and priorities. 5043 direct users of UMLS data and tools downloaded 4402 copies of the UMLS resources and issued 66 130 951 UMLS application programming interface requests in 2018. The annual reports and the scoping review results agree that the primary UMLS uses are to process and interpret text and facilitate mapping or linking between terminologies. These uses align with the original stated purpose of the UMLS.

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18

Park, Ki-Chang, Hyun-Cheol Lee, and Eun-Seok Kim. "A Software Design Method for Arduino Applications using UML." Journal of the Korea Contents Association 15, no. 8 (August 28, 2015): 1–8. http://dx.doi.org/10.5392/jkca.2015.15.08.001.

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19

Krüger, Ingolf H. "Specifying Services with UML and UML-RT." Electronic Notes in Theoretical Computer Science 65, no. 7 (May 2002): 34–50. http://dx.doi.org/10.1016/s1571-0661(04)80483-3.

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20

Trapp, Sonja, Ervin Ramollari, Matthias Heintz, Sebastian Weber, Dimitris Dranidis, and Jürgen Börstler. "Collaborative Learning of UML and SysML." International Journal of Engineering Pedagogy (iJEP) 1, no. 2 (June 30, 2011): 6. http://dx.doi.org/10.3991/ijep.v1i2.1663.

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<span style="font-size: 9.5pt; font-family: "Palatino","serif";" lang="EN-US">In t<span style="color: black;">he EU-funded project Embed4Auto, we have developed an Integrated Learning Environment (ILE) to support UML/SysML training. The ILE combines independent distance learning with collaborative problem solving and social networking. The learning environment incorporates a set of learning resources on the modeling languages UML2 and SysML, an educational modeling tool supporting class and sequence diagrams and a tool for sharing and discussing solutions to modeling exercises. First evaluations of the ILE have shown promising results.</span></span>

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21

Naegele, J. R., J. Ghijsen, R. L. Johnson, and V. Sechovsky. "Resonant Photoemission in UMn2." Physica Scripta 35, no. 6 (June 1, 1987): 877–79. http://dx.doi.org/10.1088/0031-8949/35/6/019.

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22

?�rsky, P., J. Fabian, B. A. Hess, and L. J. Schaad. "An efficient UMP2 program." Journal of Computational Chemistry 6, no. 5 (October 1985): 429–31. http://dx.doi.org/10.1002/jcc.540060509.

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23

Vasilakes, Jake, Anusha Bompelli, Jeffrey R. Bishop, Terrence J. Adam, Olivier Bodenreider, and Rui Zhang. "Assessing the enrichment of dietary supplement coverage in the Unified Medical Language System." Journal of the American Medical Informatics Association 27, no. 10 (October 1, 2020): 1547–55. http://dx.doi.org/10.1093/jamia/ocaa128.

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Abstract Objective We sought to assess the need for additional coverage of dietary supplements (DS) in the Unified Medical Language System (UMLS) by investigating (1) the overlap between the integrated DIetary Supplements Knowledge base (iDISK) DS ingredient terminology and the UMLS and (2) the coverage of iDISK and the UMLS over DS mentions in the biomedical literature. Materials and Methods We estimated the overlap between iDISK and the UMLS by mapping iDISK to the UMLS using exact and normalized strings. The coverage of iDISK and the UMLS over DS mentions in the biomedical literature was evaluated via a DS named-entity recognition (NER) task within PubMed abstracts. Results The coverage analysis revealed that only 30% of iDISK terms can be matched to the UMLS, although these cover over 99% of iDISK concepts. A manual review revealed that a majority of the unmatched terms represented new synonyms, rather than lexical variants. For NER, iDISK nearly doubles the precision and achieves a higher F1 score than the UMLS, while maintaining a competitive recall. Discussion While iDISK has significant concept overlap with the UMLS, it contains many novel synonyms. Furthermore, almost 3000 of these overlapping UMLS concepts are missing a DS designation, which could be provided by iDISK. The NER experiments show that the specialization of iDISK is useful for identifying DS mentions. Conclusions Our results show that the DS representation in the UMLS could be enriched by adding DS designations to many concepts and by adding new synonyms.

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Cuzzola, John, Ebrahim Bagheri, and Jelena Jovanovic. "UMLS to DBPedia link discovery through circular resolution." Journal of the American Medical Informatics Association 25, no. 7 (April 10, 2018): 819–26. http://dx.doi.org/10.1093/jamia/ocy021.

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Abstract Objective The goal of this work is to map Unified Medical Language System (UMLS) concepts to DBpedia resources using widely accepted ontology relations from the Simple Knowledge Organization System (skos:exactMatch, skos:closeMatch) and from the Resource Description Framework Schema (rdfs:seeAlso), as a result of which a complete mapping from UMLS (UMLS 2016AA) to DBpedia (DBpedia 2015-10) is made publicly available that includes 221 690 skos:exactMatch, 26 276 skos:closeMatch, and 6 784 322 rdfs:seeAlso mappings. Methods We propose a method called circular resolution that utilizes a combination of semantic annotators to map UMLS concepts to DBpedia resources. A set of annotators annotate definitions of UMLS concepts returning DBpedia resources while another set performs annotation on DBpedia resource abstracts returning UMLS concepts. Our pipeline aligns these 2 sets of annotations to determine appropriate mappings from UMLS to DBpedia. Results We evaluate our proposed method using structured data from the Wikidata knowledge base as the ground truth, which consists of 4899 already existing UMLS to DBpedia mappings. Our results show an 83% recall with 77% precision-at-one (P@1) in mapping UMLS concepts to DBpedia resources on this testing set. Conclusions The proposed circular resolution method is a simple yet effective technique for linking UMLS concepts to DBpedia resources. Experiments using Wikidata-based ground truth reveal a high mapping accuracy. In addition to the complete UMLS mapping downloadable in n-triple format, we provide an online browser and a RESTful service to explore the mappings.

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Lomax, Jane, and Alexa T. McCray. "Mapping the Gene Ontology Into the Unified Medical Language System." Comparative and Functional Genomics 5, no. 4 (2004): 354–61. http://dx.doi.org/10.1002/cfg.407.

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We have recently mapped the Gene Ontology (GO), developed by the Gene Ontology Consortium, into the National Library of Medicine's Unified Medical Language System (UMLS). GO has been developed for the purpose of annotating gene products in genome databases, and the UMLS has been developed as a framework for integrating large numbers of disparate terminologies, primarily for the purpose of providing better access to biomedical information sources. The mapping of GO to UMLS highlighted issues in both terminology systems. After some initial explorations and discussions between the UMLS and GO teams, the GO was integrated with the UMLS. Overall, a total of 23% of the GO terms either matched directly (3%) or linked (20%) to existing UMLS concepts. All GO terms now have a corresponding, official UMLS concept, and the entire vocabulary is available through the web-based UMLS Knowledge Source Server. The mapping of the Gene Ontology, with its focus on structures, processes and functions at the molecular level, to the existing broad coverage UMLS should contribute to linking the language and practices of clinical medicine to the language and practices of genomics.

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26

Darvishi, Ebrahim, Mohammad Javad Assari, Maryam Farhadian, Ebrahim Chavoshi, and Hamid Reza Ehsani. "Occupational exposure to mercury vapor in a compact fluorescent lamp factory: Evaluation of personal, ambient air, and biological monitoring." Toxicology and Industrial Health 35, no. 4 (March 27, 2019): 304–13. http://dx.doi.org/10.1177/0748233719831531.

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Compact fluorescent lamps (CFLs) have become a popular lighting choice in recent years despite the good performance of light-emitting diode (LED) lamps. The CFLs that have been produced recently contain 1.5–3.5 mg Hg/lamp. There is evidence that even low doses of mercury are toxic. This study aimed to assess occupational exposure to mercury vapor in workers of a CFLs factory by determining mercury levels in personal and ambient air samples and urine of workers. This cross-sectional study was conducted on 59 workers in a CFLs factory in Iran. Personal and ambient air sampling of mercury vapor levels (MVLs) was performed during a workday. In total, 10 personal samples and 10 ambient air samples of mercury vapor were collected simultaneously from different units of the factory. Urine samples were collected before the work shift. Samples were analyzed using a cold-vapor atomic absorption spectrophotometer (CVAAS). The mean of the MVLs in the personal and ambient air samples was 14.78 ± 5.76 and 67.10 ± 59.37 µg.m−3, respectively. The highest MVL was measured for the production line supervisor (25 µg.m−3). There was a significant correlation between the MVLs in the ambient air and personal samples ( r = 0.84, p = 0.005). The mean urinary mercury level (UML) was 13.85 ± 13.14 µg/g creatinine. The UML of 86.4% workers was below the 20 µg/g creatinine recommended by the Centre of Environmental and Occupational Health in Iran. There were significant differences between the UMLs in different areas of the factory ( p = 0.041). Lamp breakage was an important determinant of exposure to mercury vapor; hence, effective programs to control mercury vapor are essential in the CFLs industry.

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27

Cimino, J. J. "Use of the Unified Medical Language System in Patient Care at the Columbia-Presbyterian Medical Center." Methods of Information in Medicine 34, no. 01/02 (1995): 158–64. http://dx.doi.org/10.1055/s-0038-1634595.

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Abstract:The Unified Medical Language System (UMLS) project at the United States National Library of Medicine contains and organizes a large number of terms from controlled medical vocabularies. This study examines the suitability of the UMLS for representing patient care information as it exists in the Columbia-Presbyterian Medical Center (CPMC) clinical information system. Comparisons were made between the semantic types, semantic relations and medical concepts of the UMLS and the data model entities, semantic classes, semantic relations and concepts in the CPMC system. Results of the comparison demonstrate that the UMLS structural model is appropriate for representing CPMC vocabularies and patient data and that the UMLS concepts provide excellent coverage of CPMC concepts in many areas. Recommendations are made for enhancing UMLS structure to provide additional coverage of the CPMC model. It is concluded that content expansion to provide better coverage of clinical terminology is possible within the current UMLS model.

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28

Coleman, Derek, Viktor Ohnjec, John Artim, Erick Rivas, Jim Rumbaugh, and Rebecca Wirfs-Bracle. "UML (panel)." ACM SIGPLAN Notices 32, no. 10 (October 9, 1997): 201–5. http://dx.doi.org/10.1145/263700.263736.

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29

Spinellis, Diomidis. "UML Everywhere." IEEE Software 27, no. 5 (September 2010): 90–91. http://dx.doi.org/10.1109/ms.2010.131.

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30

Gayler, Dick, David Klappholz, Valerie J. Harvey, and Manuel A. Pérez-Quiñones. "UML tools." ACM SIGCSE Bulletin 39, no. 1 (March 7, 2007): 129–30. http://dx.doi.org/10.1145/1227504.1227356.

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31

Snook, Colin, and Michael Butler. "UML-B." ACM Transactions on Software Engineering and Methodology 15, no. 1 (January 2006): 92–122. http://dx.doi.org/10.1145/1125808.1125811.

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32

Taylor, Richard, and David Redmiles. "Argo/UML." ACM SIGSOFT Software Engineering Notes 25, no. 1 (January 2000): 97. http://dx.doi.org/10.1145/340855.341065.

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33

Kobryn, Cris. "UML 2001." Communications of the ACM 42, no. 10 (October 1999): 29–37. http://dx.doi.org/10.1145/317665.317673.

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Jung, Won-Gyo, Sang-Sung Park, Young-Geun Shin, Myoung-Hoon Kim, and Dong-Sik Jang. "Design and Implementation of Customer Management System Using UML." Journal of the Korea Contents Association 7, no. 11 (November 30, 2007): 59–68. http://dx.doi.org/10.5392/jkca.2007.7.11.059.

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35

Kim, Young-Tae, Jae-Hyun Lim, and Chi-Su Kim. "The Modification of UML for Developing of the Efficient Ontology." Journal of the Korea Academia-Industrial cooperation Society 9, no. 2 (April 30, 2008): 415–21. http://dx.doi.org/10.5762/kais.2008.9.2.415.

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Kung, Sang-Hwan. "UML based Documentation for GLORY Software Architecture." Journal of the Korea Academia-Industrial cooperation Society 10, no. 8 (August 31, 2009): 1970–76. http://dx.doi.org/10.5762/kais.2009.10.8.1970.

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37

Xu, Dongfang, Manoj Gopale, Jiacheng Zhang, Kris Brown, Edmon Begoli, and Steven Bethard. "Unified Medical Language System resources improve sieve-based generation and Bidirectional Encoder Representations from Transformers (BERT)–based ranking for concept normalization." Journal of the American Medical Informatics Association 27, no. 10 (July 27, 2020): 1510–19. http://dx.doi.org/10.1093/jamia/ocaa080.

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Abstract Objective Concept normalization, the task of linking phrases in text to concepts in an ontology, is useful for many downstream tasks including relation extraction, information retrieval, etc. We present a generate-and-rank concept normalization system based on our participation in the 2019 National NLP Clinical Challenges Shared Task Track 3 Concept Normalization. Materials and Methods The shared task provided 13 609 concept mentions drawn from 100 discharge summaries. We first design a sieve-based system that uses Lucene indices over the training data, Unified Medical Language System (UMLS) preferred terms, and UMLS synonyms to generate a list of possible concepts for each mention. We then design a listwise classifier based on the BERT (Bidirectional Encoder Representations from Transformers) neural network to rank the candidate concepts, integrating UMLS semantic types through a regularizer. Results Our generate-and-rank system was third of 33 in the competition, outperforming the candidate generator alone (81.66% vs 79.44%) and the previous state of the art (76.35%). During postevaluation, the model’s accuracy was increased to 83.56% via improvements to how training data are generated from UMLS and incorporation of our UMLS semantic type regularizer. Discussion Analysis of the model shows that prioritizing UMLS preferred terms yields better performance, that the UMLS semantic type regularizer results in qualitatively better concept predictions, and that the model performs well even on concepts not seen during training. Conclusions Our generate-and-rank framework for UMLS concept normalization integrates key UMLS features like preferred terms and semantic types with a neural network–based ranking model to accurately link phrases in text to UMLS concepts.

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McCray, Alexa T. "An Upper-Level Ontology for the Biomedical Domain." Comparative and Functional Genomics 4, no. 1 (2003): 80–84. http://dx.doi.org/10.1002/cfg.255.

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At the US National Library of Medicine we have developed the Unified Medical Language System (UMLS), whose goal it is to provide integrated access to a large number of biomedical resources by unifying the vocabularies that are used to access those resources. The UMLS currently interrelates some 60 controlled vocabularies in the biomedical domain. The UMLS coverage is quite extensive, including not only many concepts in clinical medicine, but also a large number of concepts applicable to the broad domain of the life sciences. In order to provide an overarching conceptual framework for all UMLS concepts, we developed an upper-level ontology, called the UMLS semantic network. The semantic network, through its 134 semantic types, provides a consistent categorization of all concepts represented in the UMLS. The 54 links between the semantic types provide the structure for the network and represent important relationships in the biomedical domain. Because of the growing number of information resources that contain genetic information, the UMLS coverage in this area is being expanded. We recently integrated the taxonomy of organisms developed by the NLM's National Center for Biotechnology Information, and we are currently working together with the developers of the Gene Ontology to integrate this resource, as well. As additional, standard, ontologies become publicly available, we expect to integrate these into the UMLS construct.

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Antipov, I., W. Hersh, C. A. Smith, M. Mailhot, and H. J. Lowe. "Automated Semantic Indexing of Imaging Reports to Support Retrieval of Medical Images in the Multimedia Electronic Medical Record." Methods of Information in Medicine 38, no. 04/05 (1999): 303–7. http://dx.doi.org/10.1055/s-0038-1634413.

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AbstractThis paper describes preliminary work evaluating automated semantic indexing of radiology imaging reports to represent images stored in the Image Engine multimedia medical record system at the University of Pittsburgh Medical Center. The authors used the SAPHIRE indexing system to automatically identify important biomedical concepts within radiology reports and represent these concepts with terms from the 1998 edition of the U.S. National Library of Medicine’s Unified Medical Language System (UMLS) Metathesaurus. This automated UMLS indexing was then compared with manual UMLS indexing of the same reports. Human indexing identified appropriate UMLS Metathesaurus descriptors for 81% of the important biomedical concepts contained in the report set. SAPHIRE automatically identified UMLS Metathesaurus descriptors for 64% of the important biomedical concepts contained in the report set. The overall conclusions of this pilot study were that the UMLS metathesaurus provided adequate coverage of the majority of the important concepts contained within the radiology report test set and that SAPHIRE could automatically identify and translate almost two thirds of these concepts into appropriate UMLS descriptors. Further work is required to improve both the recall and precision of this automated concept extraction process.

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Kambow, Lavleen. "Transformation of UML Class Diagram to UML Sequence Diagram." International Journal of Applied Information Systems 2, no. 9 (June 13, 2012): 19–22. http://dx.doi.org/10.5120/ijais12-450413.

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da Silva, P. P., and N. W. Paton. "User interface modeling in UMLi." IEEE Software 20, no. 4 (July 2003): 62–69. http://dx.doi.org/10.1109/ms.2003.1207457.

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Bishop, Charles W. "Alternate Approaches to a UMLS." Medical Decision Making 11, no. 4_suppl (December 1991): S99—S102. http://dx.doi.org/10.1177/0272989x9101104s19.

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A scheme for the continuing development of Meta-1, a taxonomy of medical subjects based on MeSH and other systems, is described. The objective is a single, structured classification for medical knowledge.

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Zong Chen, Y. Perl, M. Halper, J. Geller, and Huanying Gu. "Partitioning the UMLS semantic network." IEEE Transactions on Information Technology in Biomedicine 6, no. 2 (June 2002): 102–8. http://dx.doi.org/10.1109/titb.2002.1006296.

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Saripalle, Rishi, Mehdi Sookhak, and Mahboobeh Haghparast. "An Interoperable UMLS Terminology Service Using FHIR." Future Internet 12, no. 11 (November 16, 2020): 199. http://dx.doi.org/10.3390/fi12110199.

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The Unified Medical Language System (UMLS) is an internationally recognized medical vocabulary that enables semantic interoperability across various biomedical terminologies. To use its knowledge, the users must understand its complex knowledge structure, a structure that is not interoperable or is not compliant with any known biomedical and healthcare standard. Further, the users also need to have good technical skills to understand its inner working and interact with UMLS in general. These barriers might cause UMLS usage concerns among inter-disciplinary users in biomedical and healthcare informatics. Currently, there exists no terminology service that normalizes UMLS’s complex knowledge structure to a widely accepted interoperable healthcare standard and allows easy access to its knowledge, thus hiding its workings. The objective of this research is to design and implement a light-weight terminology service that allows easy access to UMLS knowledge structured using the fast health interoperability resources (FHIR) standard, a widely accepted interoperability healthcare standard. The developed terminology service, named UMLS FHIR, leverages FHIR resources and features, and can easily be integrated into any application to consume UMLS knowledge in the FHIR format without the need to understand UMLS’s native knowledge structure and its internal working.

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Humphreys, B. L., A. T. McCray, and D. A. B. Lindberg. "The Unified Medical Language System." Methods of Information in Medicine 32, no. 04 (1993): 281–91. http://dx.doi.org/10.1055/s-0038-1634945.

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AbstractIn 1986, the National Library of Medicine began a long-term research and development project to build the Unified Medical Language System® (UMLS®). The purpose of the UMLS is to improve the ability of computer programs to “understand” the biomedical meaning in user inquiries and to use this understanding to retrieve and integrate relevant machine-readable information for users. Underlying the UMLS effort is the assumption that timely access to accurate and up-to-date information will improve decision making and ultimately the quality of patient care and research. The development of the UMLS is a distributed national experiment with a strong element of international collaboration. The general strategy is to develop UMLS components through a series of successive approximations of the capabilities ultimately desired. Three experimental Knowledge Sources, the Metathesaurus®, the Semantic Network, and the Information Sources Map have been developed and are distributed annually to interested researchers, many of whom have tested and evaluated them in a range of applications. The UMLS project and current developments in high-speed, high-capacity international networks are converging in ways that have great potential for enhancing access to biomedical information.

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Humphreys, B. L., A. T. McCray, and D. A. B. Lindberg. "The Unified Medical Language System." Yearbook of Medical Informatics 02, no. 01 (August 1993): 41–51. http://dx.doi.org/10.1055/s-0038-1637976.

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AbstractIn 1986, the National Library of Medicine began a long-term research and development project to build the Unified Medical Language System® (UMLS®). The purpose of the UMLS is to improve the ability of computer programs to “understand” the biomedical meaning in user inquiries and to use this understanding to retrieve and integrate relevant machine-readable information for users. Underlying the UMLS effort is the assumption that timely access to accurate and up-to-date information will improve decision making and ultimately the quality of patient care and research. The development of the UMLS is a distributed national experiment with a strong element of international collaboration. The general strategy is to develop UMLS components through a series of successive approximations of the capabilities ultimately desired. Three experimental Knowledge Sources, the Metathesaurus®, the Semantic Network, and the Information Sources Map have been developed and are distributed annually to interested researchers, many of whom have tested and evaluated them in a range of applications. The UMLS project and current developments in high-speed, high-capacity international networks are converging in ways that have great potential for enhancing access to biomedical information.

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Jing, Xia. "The Unified Medical Language System at 30 Years and How It Is Used and Published: Systematic Review and Content Analysis." JMIR Medical Informatics 9, no. 8 (August 27, 2021): e20675. http://dx.doi.org/10.2196/20675.

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Background The Unified Medical Language System (UMLS) has been a critical tool in biomedical and health informatics, and the year 2021 marks its 30th anniversary. The UMLS brings together many broadly used vocabularies and standards in the biomedical field to facilitate interoperability among different computer systems and applications. Objective Despite its longevity, there is no comprehensive publication analysis of the use of the UMLS. Thus, this review and analysis is conducted to provide an overview of the UMLS and its use in English-language peer-reviewed publications, with the objective of providing a comprehensive understanding of how the UMLS has been used in English-language peer-reviewed publications over the last 30 years. Methods PubMed, ACM Digital Library, and the Nursing & Allied Health Database were used to search for studies. The primary search strategy was as follows: UMLS was used as a Medical Subject Headings term or a keyword or appeared in the title or abstract. Only English-language publications were considered. The publications were screened first, then coded and categorized iteratively, following the grounded theory. The review process followed the PRISMA (Preferred Reporting Items for Systematic Reviews and Meta-Analyses) guidelines. Results A total of 943 publications were included in the final analysis. Moreover, 32 publications were categorized into 2 categories; hence the total number of publications before duplicates are removed is 975. After analysis and categorization of the publications, UMLS was found to be used in the following emerging themes or areas (the number of publications and their respective percentages are given in parentheses): natural language processing (230/975, 23.6%), information retrieval (125/975, 12.8%), terminology study (90/975, 9.2%), ontology and modeling (80/975, 8.2%), medical subdomains (76/975, 7.8%), other language studies (53/975, 5.4%), artificial intelligence tools and applications (46/975, 4.7%), patient care (35/975, 3.6%), data mining and knowledge discovery (25/975, 2.6%), medical education (20/975, 2.1%), degree-related theses (13/975, 1.3%), digital library (5/975, 0.5%), and the UMLS itself (150/975, 15.4%), as well as the UMLS for other purposes (27/975, 2.8%). Conclusions The UMLS has been used successfully in patient care, medical education, digital libraries, and software development, as originally planned, as well as in degree-related theses, the building of artificial intelligence tools, data mining and knowledge discovery, foundational work in methodology, and middle layers that may lead to advanced products. Natural language processing, the UMLS itself, and information retrieval are the 3 most common themes that emerged among the included publications. The results, although largely related to academia, demonstrate that UMLS achieves its intended uses successfully, in addition to achieving uses broadly beyond its original intentions.

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Zheng, Ling, Zhe He, Duo Wei, Vipina Keloth, Jung-Wei Fan, Luke Lindemann, Xinxin Zhu, James J. Cimino, and Yehoshua Perl. "A review of auditing techniques for the Unified Medical Language System." Journal of the American Medical Informatics Association 27, no. 10 (August 7, 2020): 1625–38. http://dx.doi.org/10.1093/jamia/ocaa108.

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Abstract Objective The study sought to describe the literature related to the development of methods for auditing the Unified Medical Language System (UMLS), with particular attention to identifying errors and inconsistencies of attributes of the concepts in the UMLS Metathesaurus. Materials and Methods We applied the PRISMA (Preferred Reporting Items for Systematic Reviews and Meta-Analyses) approach by searching the MEDLINE database and Google Scholar for studies referencing the UMLS and any of several terms related to auditing, error detection, and quality assurance. A qualitative analysis and summarization of articles that met inclusion criteria were performed. Results Eighty-three studies were reviewed in detail. We first categorized techniques based on various aspects including concepts, concept names, and synonymy (n = 37), semantic type assignments (n = 36), hierarchical relationships (n = 24), lateral relationships (n = 12), ontology enrichment (n = 8), and ontology alignment (n = 18). We also categorized the methods according to their level of automation (ie, automated systematic, automated heuristic, or manual) and the type of knowledge used (ie, intrinsic or extrinsic knowledge). Conclusions This study is a comprehensive review of the published methods for auditing the various conceptual aspects of the UMLS. Categorizing the auditing techniques according to the various aspects will enable the curators of the UMLS as well as researchers comprehensive easy access to this wealth of knowledge (eg, for auditing lateral relationships in the UMLS). We also reviewed ontology enrichment and alignment techniques due to their critical use of and impact on the UMLS.

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Price, Rosanne, Nectaria Tryfona, and Christian S. Jensen. "Extended Spatiotemporal UML." Journal of Database Management 11, no. 4 (October 2000): 14–27. http://dx.doi.org/10.4018/jdm.2000100102.

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Reinhartz-Berger, Iris, and Arnon Sturm. "Enhancing UML Models." Journal of Database Management 19, no. 1 (January 2008): 74–94. http://dx.doi.org/10.4018/jdm.2008010104.

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