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Developing and accessing scientific databases with the Object-Protocol Model (OPM) data management tools

I.-M.A. Chen, A.S. Kosky, V.M. Markowitz, E. Szeto
Proceedings. Ninth International Conference on Scientific and Statistical Database Management (Cat. No.97TB100150)  
The Object-Protocol Model (OPM) data management tools provide facilities for rapid development, documentation, and flexible exploration of scientific databases.  ...  The tools are based on OPM, an object-oriented data model which is similar to the ODMG standard, but also supports extensions for modeling scientific data [41.  ...  This work is supported by the Office of Health and Environmental Research Program and the Mathematical, Information, and Computational Sciences Division of the Office of Energy Research , U.S.  ... 
doi:10.1109/ssdm.1997.621167 dblp:conf/ssdbm/ChenKMS97 fatcat:tuy2jevelzamjgofxodu7fowpi

Storing, reasoning, and querying OPM-compliant scientific workflow provenance using relational databases

Chunhyeok Lim, Shiyong Lu, Artem Chebotko, Farshad Fotouhi
2011 Future generations computer systems  
In this paper, we present OPMProv, a relational database-based scientific workflow provenance system, that is fully compliant with OPM (v1.01).  ...  Our main contributions are: i) we design an entity-relationship diagram for OPM and translate it into a relational database schema for the storage of provenance; ii) we propose an efficient data mapping  ...  Acknowledgments The authors would like to thank Girish Subramanian from Indiana University for helping us set up the provenance database of Karma.  ... 
doi:10.1016/j.future.2010.10.013 fatcat:mdzm4lhc7fcmpir6xxvvnb4nvm

OPM: Object-Protocol Model Data Management Tools '97 [chapter]

Victor M. Markowitz, I-Min A. Chen, Anthony S. Kosky, Ernest Szeto
Bioinformatics: Databases and Systems  
Acknowledgments Between 1992 and 1997, the OPM tool development was carried out in the framework of the Data Management R&D Group at Lawrence Berkeley National Laboratory (LBNL), with funding provided  ...  We want to thank Arie Shoshani, the head of the Data Management R&D Group at LBNL, for his active support and encouragement. References  ...  Introduction The development of the Object-Protocol Model (OPM) and OPM data management tools started in 1992.  ... 
doi:10.1007/0-306-46903-0_17 fatcat:5ofpjazozrf53n76cnoadqp2na

Cézeaux-Aulnat-Opme-Puy De Dôme: a multi-site for the long-term survey of the tropospheric composition and climate change

Jean-Luc Baray, Laurent Deguillaume, Aurélie Colomb, Karine Sellegri, Evelyn Freney, Clémence Rose, Joël Van Baelen, Jean-Marc Pichon, David Picard, Patrick Fréville, Laëtitia Bouvier, Mickaël Ribeiro (+42 others)
2020 Atmospheric Measurement Techniques  
It is also an ideal place to study cloud properties with frequent presence of clouds at the top in fall and winter.  ...  The site located on top of the puy de Dôme mountain (1465 m a.s.l.) is completed by additional sites located at lower altitudes and adding the vertical dimension to the atmospheric observations: Opme (  ...  We thank all the people who contributed to the functioning and development of the instrumented site CO-PDD without being a co-author of this article. . 654109) ).  ... 
doi:10.5194/amt-13-3413-2020 fatcat:brklxmldobbqdbsy2cxxkdsrcy

3DBase – a macromolecular structure database

E. E. Abola, J. Prilusky, N. O. Manning, J. L. Sussman
1996 Acta Crystallographica Section A Foundations of Crystallography  
The PDB is supported by a combination of Federal Government Agency funds and user fees. Support is provided by the U.S. National Science Foundation, the U.S.  ...  National Institutes of General Medical Sciences, National Library of Medicine, and the U.S. Department of Energy under contract DE-AC02-76CHOOO 16.  ...  DBMS and the Object Protocol Model (OPM) and OPM data management tools developed by Victor Markowitz's group at Lawrence Berkeley National Laboratory.  ... 
doi:10.1107/s0108767396076180 fatcat:fwjwpe35kjhxbm2shxxj7uwwlq

Protein Data Bank – where we are today

N. O. Manning, E. E. Abola, F. C. Bernstein, J. A. Callaway, F. M. Cummings, B. R. Deroski, P. A. Esposito, A. Forman, P. A. Langdon, M. D. Libeson, J. E. McCarthy, J. Prilusky (+7 others)
1996 Acta Crystallographica Section A Foundations of Crystallography  
The PDB is supported by a combination of Federal Government Agency funds and user fees. Support is provided by the U.S. National Science Foundation, the U.S.  ...  National Institutes of General Medical Sciences, National Library of Medicine, and the U.S. Department of Energy under contract DE-AC02-76CHOOO 16.  ...  DBMS and the Object Protocol Model (OPM) and OPM data management tools developed by Victor Markowitz's group at Lawrence Berkeley National Laboratory.  ... 
doi:10.1107/s0108767396076179 fatcat:ns2x6m7rmfamhebfymfui6vml4

Advanced query mechanisms for biological databases

I M Chen, A S Kosky, V M Markowitz, E Szeto, T Topaloglou
1998 Proceedings. International Conference on Intelligent Systems for Molecular Biology  
, and notations, in the framework of the Object-Protocol Model (OPM).  ...  These tools avoid the restrictions imposed by traditional fixed-form query interfaces, while providing users with simple and intuitive facilities for formulating ad-hoc queries across heterogeneous databases  ...  The work presented in this paper was carried out while the authors were affiliated with the Lawrence Berkeley National Laboratory, with support provided by the Office of Health and Environmental Research  ... 
pmid:9783208 fatcat:r4phgte7lvcczlgynn6ekvoknu

The Protein Data Bank: Current status and future challenges

E.E. Abola, N.O. Manning, J. Prilusky, D.R. Stampf, J.L. Sussman
1996 Journal of Research of the National Institute of Standards and Technology  
The PDB is now being transformed into 3DB, the Three-Dimensional Database of Biomacromolecular Structures, with significantly enhanced capabilities.  ...  The Protein Data Bank (PDB) is an archive of experimentally determined, three-dimensional structures of proteins, nucleic acids, and other biological macromolecules.  ...  for 3DB The 3DBase is constructed with the SYBASE RDBMS, the Object-Protocol Model (OPM), and the OPM data management tools [14] developed by Victor Markowitz's group at Lawrence Berkeley National Laboratory  ... 
doi:10.6028/jres.101.025 pmid:27805161 pmcid:PMC4963140 fatcat:l6jpapo5kbci7cebtchogylvoi

Using Provenance to support Good Laboratory Practice in Grid Environments [article]

Miriam Ney and Guy K. Kloss and Andreas Schreiber
2011 arXiv   pre-print
As a new approach to this, a scientific data management system (DataFinder) is enhanced with features for traceable documentation.  ...  Due to computerised research systems, acquired data became more elaborate, thus increasing the need for electronic notebooks with data storage, computational features and reliable electronic documentation  ...  To overcome this situation common in many research institutes, the DLR facility Simulation and Software Technology has developed the scientific data management system DataFinder (cf. [20] ).  ... 
arXiv:1112.3062v1 fatcat:whvr52ouqzdsbmi3ap6nrthxga

DataFoundry: information management for scientific data

T. Critchlow, K. Fidelis, M. Ganesh, R. Musick, T. Slezak
2000 IEEE Transactions on Information Technology in Biomedicine  
First, schema integration is more difficult for scientific databases than for business sources, because of the complexity of the concepts and the associated relationships.  ...  They have proven to be invaluable tools by integrating information from distributed, heterogeneous sources and summarizing this data for use throughout the enterprise.  ...  The Object Protocol Model (OPM) [6] , developed at Lawrence Berkeley National Laboratory, provides a set of tools for scientific data management.  ... 
doi:10.1109/4233.826859 pmid:10761774 fatcat:c5xfzvai65gzxmhjxptxj65mfe

Research Traceability using Provenance Services for Biomedical Analysis [article]

Ashiq Anjum, Peter Bloodsworth, Andrew Branson, Irfan Habib, Richard McClatchey, Tony Solomonides, the neuGRID Consortium
2014 arXiv   pre-print
We outline the approach being developed in the neuGRID project to use provenance management techniques for the purposes of capturing and preserving the provenance data that emerges in the specification  ...  approach for provenance management could emerge for more generic application to the (Health)Grid community.  ...  The OPM also enables developers to develop and share tools that work across systems. To implement OPM compliance, there are essentially three steps:  Describe an application specific schema.  ... 
arXiv:1403.0230v1 fatcat:xfhuf4mghvakfl4cyhkc5mjxm4

Embedding Data within Knowledge Spaces [article]

James D. Myers, Joe Futrelle, Jeff Gaynor, Joel Plutchak, Peter Bajcsy, Jason Kastner, Kailash Kotwani, Jong Sung Lee, Luigi Marini, Rob Kooper, Robert E. McGrath, Terry McLaren (+3 others)
2009 arXiv   pre-print
We have developed the open-source Tupelo semantic content management framework and are employing it to manage a wide range of e-Science entities (including data, documents, workflows, people, and projects  ...  The promise of e-Science will only be realized when data is discoverable, accessible, and comprehensible within distributed teams, across disciplines, and over the long-term--without reliance on out-of-band  ...  Any opinions, findings, and conclusions or recommendations expressed in this publication are those of the author(s) and do not necessarily reflect the views of NSF and ONR.  ... 
arXiv:0902.0744v1 fatcat:adkv7fvkvbfctnnntzsjsy4i5q

Research Traceability using Provenance Services for Biomedical Analysis [article]

Ashiq Anjum, Peter Bloodsworth, Andrew Branson, Irfan Habib, Richard McClatchey, Tony Solomonides, the neuGRID Consortium
2012 arXiv   pre-print
We outline the approach being developed in the neuGRID project to use provenance management techniques for the purposes of capturing and preserving the provenance data that emerges in the specification  ...  approach for provenance management could emerge for more generic application to the (Health)Grid community.  ...  The OPM also enables developers to develop and share tools that work across systems. To implement OPM compliance, there are essentially three steps:  Describe an application specific schema.  ... 
arXiv:1202.5517v1 fatcat:zhkhowd2pzccdjwkx56ts6emli

Experiences applying meta-data to bioinformatics

Terence Critchlow, Ron Musick, Tom Slezak
2001 Information Sciences  
Other Approaches The Object Protocol Model (OPM) [5] , developed at Lawrence Berkeley National Laboratory and licensed by Gene Logic Corp., provides a set of tools for scientific data management.  ...  The OPM tool-set consists of a schema editor, for specifying and managing OPM schemata; a graphical querying and browsing tool; and tools for conversion between relational and OPM schema so OPM can access  ...  Work performed under the auspices of the U.S. DOE by LLNL under contract No. W-7405-ENG-48 . UCRL-JC-139907  ... 
doi:10.1016/s0020-0255(01)00155-4 fatcat:hjhmsnuivbayxpev7ukuvde6xq

The KBMS Project and Beyond [chapter]

Vinay K. Chaudhri, Igor Jurisica, Manolis Koubarakis, Dimitris Plexousakis, Thodoros Topaloglou
2009 Lecture Notes in Computer Science  
The objects with a spatial extension can be placed in spaces, called maps, at variable scales and related to other spatial objects or constants through qualitative or quantitative relationships.  ...  rule management, and concurrency control.  ...  The OPM Tools Suite: The Object Protocol Model (OPM) project [53] at the Lawrence Berkeley National Laboratory utilizes a semantic data model to describe the semantics of the entities in biological databases  ... 
doi:10.1007/978-3-642-02463-4_24 fatcat:6wrere4quvgcdafnpoh5c7broy
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