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BioKleisli: Integrating Biomedical Data and Analysis Packages [chapter]

Susan B. Davidson, O. Peter Buneman, Jonathan Crabtree, Val Tannen, G. Christian Overton, Limsoon Wong
Bioinformatics: Databases and Systems  
However, currently there are no commercial tools for enabling such an integrated digital library, and a fundamental barrier to developing such tools appears to be one of language design and optimization  ...  Data of interest to biomedical researchers associated with the Human Genome Project (HGP) is stored all over the world in a variety of electronic data formats and accessible through a variety of interfaces  ...  We would like to thank Peter Buneman for his help, suggestions and examples, and Kyle Hart and Jonathan Crabtree for their implementation work on Kleisli.  ... 
doi:10.1007/0-306-46903-0_18 fatcat:coirnqnpyrhabhqd3ozkhv4afe

Biodiversity informatics: organizing and linking information across the spectrum of life

I. N. Sarkar
2007 Briefings in Bioinformatics  
BioKleisli: a digital library for biomedical researchers, Int J Digit Libr 1997;1:36-53. 42.  ...  For example, rather than GenBank keeping track of all possible vernacular and scientific names for a given organism (including misspellings), these could be made available through a Web service (such as  ...  Perhaps the most significant, relevant digitization effort currently underway is the Biodiversity Heritage Library(BHL; [42]).  ... 
doi:10.1093/bib/bbm037 pmid:17704120 fatcat:y3n5b5vdlbdjvpgcaojgvchnme

DFL designer

Jacek Sroka, Piotr Włodarczyk, Łukasz Krupa, Jan Hidders
2010 Proceedings of the 1st International Workshop on Workflow Approaches to New Data-centric Science - Wands '10  
DFL designer not only allows design and enactment of complicated COSWs with the use of a huge library of supported bioinformatics services, but also provides a set of features for testing and analyzing  ...  workflow specifications that is unique for COSWs, including but not limited to interactive firing of transitions, hierarchical analysis of COSWs and translation of side-effect free COSWs to a query language  ...  Acknowledgments: The authors thank Lukasz Krupa and Paolo Missier for their contribution to the implementation.  ... 
doi:10.1145/1833398.1833403 fatcat:5wjwu4sln5cipdtsgamupcjmre

Toward Routine Automatic Pathway Discovery from On-line Scientific Text Abstracts

Ng, Wong
We describe a prototype system for automatic pathway discovery from on-line text abstracts, combining technologies that (1) retrieve research abstracts from online sources, (2) extract relevant information  ...  We are entering a new era of research where the latest scientific discoveries are often first reported online and are readily accessible by scientists worldwide.  ...  ., BioKleisli: a digital library for biomedical researchers, International Journal of Digital Libraries, 1:36–53, 1997.  ... 
pmid:11072347 fatcat:fuxahutawzbwlck3q3ym6aps64

Page 528 of IBM Systems Journal Vol. 40, Issue 2 [page]

IBM Systems Journal  
Wong, “Biokleisli: A Digital Library for Biomedical Researchers,” Journal of Digital Libraries 1, No. 1, 36-53 (1996). . K. Hart, L. Wong, C. Overton, and P.  ...  A. Rapp, and D. Wheeler, “GenBank,” Nucleic Acids Research 28, No. 1, 15-18 (2000). . A. Bairoch and R.  ... 

Approaches to Access Biological Data Sources [chapter]

Assia Rharbi, Khadija Amine, Zohra Bakkoury, Afaf Mikou, Anass Kettani, Abdelkader Betari
2012 Lipoproteins - Role in Health and Diseases  
biomedical research.  ...  PubMed is a free search engine giving access to the MEDLINE bibliographic database, gathering citations and abstracts of biomedical research.  ... 
doi:10.5772/48740 fatcat:x5bfjcgztzaozcx2kgstma2spa

Automatic Discovery and Inferencing of Complex Bioinformatics Web Interfaces

Anne H. H. Ngu, Daniel Rocco, Terence Critchlow, David Buttler
2005 World wide web (Bussum)  
We propose a service class description (SCD)-a meta-data approach for classifying Web data sources that takes into account both the capability and the conversational semantics of the source.  ...  The World Wide Web provides a vast resource to genomics researchers, with Web-based access to distributed data sources such as BLAST sequence homology search interfaces.  ...  There is also active research into topic-driven or focused crawlers; Srinivasan et al. [25] present such a crawler for biomedical sources that includes a treatment of related systems.  ... 
doi:10.1007/s11280-005-0509-5 fatcat:lzojor4l2vfxpadnwitj2irpsq

EMBnet.journal 18 Suppl. B

EMBnet Journal
2012 EMBnet journal  
Carlo Bernasconi and the Collegio Ghislieri in Pavia for their active support.  ...  Council of Italy (CNR) and the Polish Academy of Sciences (PAN Acknowledgements This work is partial fulfillment of the research objective of "DM19410 -Laboratorio di Bioinformatica per la Biodiversità  ...  This could provide promising research pathways for the biomedical data mining community.  ... 
doi:10.14806/ej.18.b.592 fatcat:wlwsmbdlfzbjtk7vyhiabdov6q


Ling Liu, Jianjun Zhang, Wei Han, Carlton Pu, James Caverlee, Sungkeun Park, Terence Critchlow, David Buttler, Matthew Coleman
2006 International Journal of Web Services Research  
First, we explicitly separate tasks of building wrappers that are specific to a Web service from the tasks that are repetitive for any service, thus the code can be generated as a wrapper library component  ...  We present a service-oriented architecture and a set of techniques for developing wrapper code generators, including the methodology of designing an effective wrapper program construction facility and  ...  ACKNOWLEDGMENTS This work is a joint effort between the Georgia Institute of Technology Team led by Ling Liu and the LLNL team led by Terence Critchlow.  ... 
doi:10.4018/jwsr.2006040102 fatcat:osamptynhjas3nz7y2fnhnxcgy