Authority Control for Scientific Data: The Case of Molecular Biology

REFERENCES

• Allen , R. B. 2011 . “ Category-based models for knowledge representation ” . In Information: A fundamental construct Manuscript in preparation. Retrieved from http://boballen.info/ISS/
   Google Scholar
• Ananiadou , S. , Friedman , C. and Tsujii , J. 2004 . Introduction: Named entity recognition in biomedicine . Biomedical Informatics , 37 : 393 – 395 . doi:10.1016/j.jbi. 2004.08.011
   Web of Science ®Google Scholar
• Atkins , D. , Droegemeier , K. , Feldman , S. , Garcia-Molina , H. , Klein , M. , Messerschmitt , D. and Wright , M. H. 2003 . Revolutionizing science and engineering through cyberinfrastructure: Report of the National Science Foundation Blue-Ribbon Advisory Panel on Cyberinfrastructure , Arlington , VA : National Science Foundation . Retrieved from http://www.nsf.gov/od/oci/reports/atkins.pdf
   Google Scholar
• Bard , J. B. L. and Rhee , S. Y. 2004 . Ontologies in biology: Design, applications and future challenges . Nature Review Genetics , 5 : 213 – 222 . doi:10.1038/nrg 1295
   PubMed Web of Science ®Google Scholar
• Blaschke , C. , Hirschman , L. and Valencia , A. 2002 . Information extraction in molecular biology . Briefings in Bioinformatics , 3 : 154 – 165 .
   PubMedGoogle Scholar
• Bodenreider , O. 2004 . The Unified Medical Language System (UMLS): Integrating biomedical terminology . Nucleic Acids Research , 32 : D267 – D270 . doi:10.1093/ nar/gkh061
   PubMed Web of Science ®Google Scholar
• Clark , T. , Martin , S. and Liefeld , T. 2004 . Globally distributed object identification for biological knowledgebases . Briefings in Bioinformatics , 5 : 59 – 70 . doi:10.1093/ bib/5.1.59
   PubMed Web of Science ®Google Scholar
• Cohen , A. M. and Hersh , W. R. 2005 . A survey of current work in biomedical text mining . Briefings in Bioinformatics , 6 : 57 – 71 . doi:10.1093/bib/6.1.57
   PubMed Web of Science ®Google Scholar
• Crick , F. 1970 . Central dogma of molecular biology . Nature , 227 ( 5258 ) : 561 – 563 . doi:10.10381227561a0
   PubMed Web of Science ®Google Scholar
• Dalgleish , R. , Flicek , P. , Cunningham , F. , Astashyn , A. , Tully , R. E. , Proctor , G. and Maglott , D. R. 2010 . Locus Reference Genomic sequences: An improved basis for describing human DNA variants . Genome Medicine , 2 : 24 doi:10.1186/ gm145
   PubMed Web of Science ®Google Scholar
• de Bruijn , L. and Martin , J. 2002 . “ Literature mining in molecular biology ” . In Proceedings of the EFMI Workshop on Natural Language Processing in Biomedical Applications , Edited by: Baud , R. and Ruch , P. 1 – 5 . Ottawa , , Canada : National Research Council of Canada .
   Google Scholar
• den Dunnen , J. T. and Antonarakis , S. E. 2000 . Mutation nomenclature extensions and suggestions to describe complex mutations: A discussion . Human Mutation , 15 : 7 – 12 .
   PubMed Web of Science ®Google Scholar
• Elmasri , R. and Navathe , S. 2000 . Fundamentals of database systems (3rd ed.) , Reading , MA : Addison-Wesley .
   Google Scholar
• Field , D. , Garrity , G. , Gray , T. , Morrison , N. , Selengut , J. , Sterk , P. and Wipat , A. 2008 . The minimum information about a genome sequence (MIGS) specification . Nature Biotechnology , 26 : 541 – 547 . doi:10.1038/1360
   PubMed Web of Science ®Google Scholar
• Fundel , K. and Zimmer , R. 2006 . Gene and protein nomenclature in public databases . BMC Bioinformatics , 7 : 372 doi:10.1186/1471-2105-7-372
   PubMed Web of Science ®Google Scholar
• Gene Ontology . 2011 . GO ontology relations . Retrieved from http://www.gene-ontology.org/GO.ontology.relations.shtml
   Google Scholar
• Gene Ontology Consortium . 2000 . Gene Ontology: Tool for the unification of biology . Nature Genetics , 25 : 25 – 29 . doi:10.1038/75556
   PubMed Web of Science ®Google Scholar
• Genomic Standards Consortium . 2011 . Minimum Information about a (Meta) Genome Sequence Retrieved from http://gensc.org/gc_wiki/index.php/MIGS/MIMS
   Google Scholar
• Go , K. and Carroll , J. 2004a . “ Scenario-based task analysis ” . In The handbook of task analysis for human-computer interaction , Edited by: Diaper , D. and Stanton , N. 117 – 133 . Mahwah , NJ : Lawrence Erlbaum .
   Google Scholar
• Go , K. and Carroll , J. 2004b . The blind men and the elephant: Views of scenario-based system design . Interactions , 11 ( 6 ) : 44 – 53 . doi:10.1145/1029036.1029037
   Google Scholar
• Goll , J. , Montgomery , R. , Brinkac , L. M. , Schobel , S. , Harkins , D. M. , Sebastian , Y. and Sutton , G. 2010 . The Protein Naming Utility: A rules database for protein nomenclature . Nucleic Acids Research , 38 : D336 – D339 . doi:10.1093/nar/ gkp958
   Web of Science ®Google Scholar
• Gorman , M. 2004 . Authority control in the context of bibliographic control in the electronic environment . Cataloging & Classification Quarterly , 38 ( 3–4 ) : 11 – 22 . doi:10.1300/J104v38n03_03
   Google Scholar
• Greenberg , J. 2009 . Theoretical considerations of lifecycle modeling: An analysis of the Dryad Repository demonstrating automatic metadata propagation, inheritance, and value system adoption . Cataloging & Classification Quarterly , 47 : 380 – 402 . doi:10.1080/01639370902737547
   Google Scholar
• Gulley , M. L. , Braziel , R. M. , Halling , K. C. , His , E. D. , Kant , J. A , Nikiforova , M. N. and Versalovic , J. 2007 . Clinical laboratory reports in molecular pathology . Archives of Pathology & Laboratory Medicine , 131 : 852 – 863 .
   PubMed Web of Science ®Google Scholar
• Higgs , P. G. and Attwood , T. K. 2005 . Bioinformatics and molecular evolution , Malden , MA : Blackwell .
   Google Scholar
• Hodge , G. 2000 . Systems of knowledge organization for digital libraries: Beyond traditional authority files (CLIR Report 91) , Washington , DC : Council on Library and Information Resources . Retrieved from http://www.clir.org/pubs/reports/pub91/pub91.pdf
   Google Scholar
• Institute for Museum and Library Services . 2011 . Specifications for projects that develop digital products Retrieved from http://www.imls.gov/assets/1/AssetManager/DigitalProducts.pdf
   Google Scholar
• International Federation of Library Associations and Institutions . 2009 . Functional requirements for bibliographic records: Final report Retrieved from http://archive.ifla.org/VII/s13/frbr/frbr_2008.pdf
   Google Scholar
• Joint Steering Committee for Development of RDA (Ed.) . 2009 . RDA scope and structure , Chicago , IL : American Library Association . Retrieved from http://www.rda-jsc.org/docs/5rda-scoperev4.pdf
   Google Scholar
• Juran , J. 1992 . Juran on quality by design , New York , NY : Free Press .
   Google Scholar
• Khatri , P. , Sellamuthu , S. , Malhotra , P. , Amin , K. , Done , A. and Draghici , S. 2005 . Recent additions and improvements to the Onto-Tools . Nucleic Acids Research , 33 : W762 – W765 . doi:10.1093/nar/gki472
   PubMed Web of Science ®Google Scholar
• Krallinger , M. , Erhardt , R. A. and Valencia , A. March 2005 . Text-mining approaches in molecular biology and biomedicine . Drug Discovery Today , 10 : 439 – 445 . doi:10.1016/S1359-6446(05)03376-3
   PubMed Web of Science ®Google Scholar
• Krallinger , M. , Valencia , A. and Hirschman , L. 2008 . Linking genes to literature: Text mining, information extraction, and retrieval applications for biology . Genome Biology , 9 ( Suppl. 2 ) : S8 – S8 . 14. doi:10.1186/gb-2008-9-S2-S8
   Web of Science ®Google Scholar
• Lambe , P. 2007 . Organising knowledge: Taxonomies, knowledge and organisational effectiveness , Oxford , , United Kingdom : Chadons .
   Google Scholar
• Liu , H. , Hu , Z. , Zhang , J. and Wu , C. 2006 . BioThesaurus: A web-based thesaurus of protein and gene names . Bioinformatics , 22 : 103 – 105 . doi:10.1093/bioinfor- matics/bti749
   PubMed Web of Science ®Google Scholar
• MacMullen , W. J. and Denn , S. O. 2005 . Information problems in molecular biology and bioinformatics . Journal of the American Society for Information Science and Technology , 56 : 447 – 456 . doi:10.1002/asi.20134
   Web of Science ®Google Scholar
• Martin , S. , Hohman , M. M. and Liefeld , T. 2005 . The impact of life science identifier on informatics data . Drug Discovery Today , 10 : 1566 – 1572 . doi:10.1016/S1359-6446(05)03651-2
   PubMed Web of Science ®Google Scholar
• National Endowment for the Humanities . 2011 . Guidance for data management plans for NEH Office of Digital Humanities proposals and awards Retrieved from http://www.neh.gov/grants/guidelines/pdf/DataManagementPlans.pdf
   Google Scholar
• National Institutes of Health . 2010 . NIH data sharing policy and implementation guidance (NIH Publication No. 03–05-2003) , Bethesda , MD : Author . Retrieved from http://grants.nih.gov/grants/policy/data_sharing/data_sharing_guidance.htm#goals
   Google Scholar
• National Library of Medicine . 2009 . UMLS reference manual , Bethesda , MD : Author . Retrieved from http://www.ncbi.nlm.nih.gov/books/NBK9675/
   Google Scholar
• National Science Board . 2005 . Long-lived digital data collections: Enabling research and education in the 21st century (NSB Report No. 05–40) , Arlington , VA : National Science Foundation . Retrieved from http://www.nsf.gov/pubs/2005/nsb0540/nsb0540.pdf
   Google Scholar
• National Science Foundation . 2007 . Cyberinfrastructure vision for 21st century discovery (NSF Report No. 07–28) , Arlington , VA : Author . Retrieved from http://www.nsf.gov/pubs/2007/nsf0728/nsf0728.pdf
   Google Scholar
• National Science Foundation . 2010 . Grant proposal guide (NSF Publication No. gpg11001) , Arlington , VA : Author . Retrieved from http://www.nsf.gov/pubs/policydocs/pappguide/nsf11001/gpgprint.pdf
   Google Scholar
• Open Biological and Biomedical Ontologies . 2011 . Archive of original principles Retrieved from http://www.obofoundry.org/crit_2006.shtml
   Google Scholar
• Patton , G. 2009 . Functional requirements for authority data: A conceptual model (FRAD) IFLA Working Group on the Functional Requirements and Numbering of Authority Records (FRANAR). IFLA Series on Bibliographic Control (Vol. 34). München: K. G. Saur
   Google Scholar
• Patterson , D. J. , Cooper , J. , Kirk , P. M. , Pyle , R. L. and Remsen , D. P. 2010 . Names are key to the big new biology . Trends in Ecology and Evolution , 25 : 686 – 691 . doi: 10.1016/j.tree.2010.09.004
   PubMed Web of Science ®Google Scholar
• Pruitt , K. D. , Tatusova , T. , Klimke , W. and Maglott , D. R. 2009 . NCBI Reference Sequences: Current status, policy and new initiatives . Nucleic Acid Research , 37 : D32 – D36 . doi:10.1093/nar/gkn721
   PubMed Web of Science ®Google Scholar
• Pruitt , K. D. , Tatusova , T. and Maglott , D. R. 2005 . NCBI Reference Sequence (RefSeq): A curated non-redundant sequence database of genomes, transcripts and proteins . Nucleic Acids Research , 33 : D501 – D504 . doi:10.1093/nar/gki025
   PubMed Web of Science ®Google Scholar
• San Gil , I. , Hutchison , V. , Frame , M. and Palanisamy , G. 2010 . Metadata activities in biology . Journal of Library Metadata , 10 : 99 – 118 . doi:10.1080/19386389. 506389
   Google Scholar
• Seal , R. L. , Gordon , S. M. , Lush , M. J. , Wright , M. W. and Bruford , E. A. 2011 . Genenames.org: The HGNC resources in 2011 . Nucleic Acids Research , 39 : D514 – D519 . doi:10.1093/nar/gkq892
   Web of Science ®Google Scholar
• Smalheiser , N. and Torvik , V. 2009 . Author name disambiguation . Annual Review of Information Science and Technology (ARIST) , 43 : 1 – 43 . doi:10.1002/ aris.2009.1440430113
   Google Scholar
• Smith , B. , Ashburner , M. , Rosse , C. , Bard , J. , Bug , W. , Ceusters , W. and Lewis , S. 2007 . The OBO Foundry: Coordinated evolution of ontologies to support biomedical data integration . Nature Biotechnology , 25 : 1251 – 1255 . doi:10.1038/nbt-1346
   PubMed Web of Science ®Google Scholar
• Stvilia , B. , Gasser , L. , Twidale , M. and Smith , L. C. 2007 . A framework for information quality assessment . Journal of the American Society for Information Science and Technology , 58 : 1720 – 1733 . doi:10.1002/asi.20652
   Web of Science ®Google Scholar
• Svenonius , E. 1986 . Unanswered questions in the design of controlled vocabularies . Journal of the American Society for Information Science , 37 : 331 – 340 .
   Web of Science ®Google Scholar
• Tillett , B. 2004 . Authority control: State of the art and new perspectives . Cataloging & Classification Quarterly , 38 ( 3–4 ) : 23 – 41 . doi:10.1300/J104v38n03_04
   Google Scholar
• Turner , P. , McLennan , A. , Bates , A. and White , M. 2005 . Molecular biology (3rd ed.) , New York , NY : Taylor & Francis .
   Google Scholar
• Unified Medical Language System . 2011 . Metathesaurus release statistics Retrieved from http://www.nlm.nih.gov/research/umls/knowledge_sources/metathesaurus/release/statistics.html
   Google Scholar
• UniProt Consortium . 2011 . Protein naming guidelines , Washington , DC : Author . Retrieved from http://www.uniprot.org/docs/nameprot
   Google Scholar
• Wain , H. M. , Bruford , E. A. , Lovering , R. C. , Lush , M. J. , Wright , M. W. and Povey , S. 2002 . Guidelines for human gene nomenclature . Genomics , 79 : 464 – 470 . doi: 10.1006/geno.2002.6748
   PubMed Web of Science ®Google Scholar
• Wand , Y. and Wang , R. 1996 . Anchoring data quality dimensions in ontological foundations . Communications of the ACM , 39 ( 11 ) : 86 – 92 .
   Web of Science ®Google Scholar
• Wang , R. and Strong , D. 1996 . Beyond accuracy: What data quality means to data consumers . Journal of Management Information Systems , 12 ( 4 ) : 5 – 35 .
   Google Scholar
• Yilmaz , P. , Gilbert , J. A. , Knight , R. , Amaral-Zettler , L. , Karsch-Mizrachi , I. , Cochrane , G. and Field , D. 2011 . The genomic standards consortium: Bringing standards to life for microbial ecology . The ISME Journal , 5 : 1565 – 1567 . doi:10.1038/ismej. 2011.39
   PubMed Web of Science ®Google Scholar
• Yilmaz , P. , Kottmann , R. , Field , D. , Knight , R. , Cole , J. R. , Amaral-Zettler , L. and Glöckner , F. O. 2011 . Minimum information about a marker gene sequence (MIMARKS) and minimum information about any (x) sequence (MIxS) specifications . Nature Biotechnology , 29 : 415 – 420 . doi:10.1038/nbt.1823
   PubMed Web of Science ®Google Scholar