OpenWetWare:Steering committee/NSF BDI Grant/openwetware.bib

-- This is a Bibtex file. See /all.tex/ for this complete formatted citation list. @inproceedings{Aumueller::2005, Author = {David Aumueller}, Booktitle = {2nd European Semantic Web Conference 2005 (ESWC2005)}, Date-Added = {2006-07-06 01:52:17 -0400}, Date-Modified = {2006-07-06 01:53:13 -0400}, Title = {Semantic Authoring and Retrieval within a Wiki}, Url = {http://the.navigable.info/2005/aumueller05wiksar.pdf}, Year = {2005}}

@inproceedings{Bergin:2002, Address = {New York, NY, USA}, Author = {Joseph Bergin}, Booktitle = {ITiCSE '02: Proceedings of the 7th annual conference on Innovation and technology in computer science education}, Doi = {http://doi.acm.org/10.1145/544414.544473}, Isbn = {1-58113-499-1}, Location = {Aarhus, Denmark}, Pages = {195--195}, Publisher = {ACM Press}, Title = {Teaching on the wiki web}, Year = {2002}}

@misc{Berman:Nat-Struct-Biol:2003, Aid = {nsb1203-980 [pii]}, Au = {Berman H and Henrick K and Nakamura H}, Author = {Berman, Helen and Henrick, Kim and Nakamura, Haruki}, Da = {20031124}, Date-Modified = {2006-07-06 01:00:02 -0400}, Dcom = {20040202}, Edat = {2003/11/25 05:00}, Ip = {12}, Jid = {9421566}, Journal = {Nat Struct Biol}, Jt = {Nature structural biology.}, Keywords = {Archives, Computational Biology, Databases, Protein/*trends, International Agencies}, Language = {eng}, Mhda = {2004/02/03 05:00}, Number = {1072-8368 (Print)}, Own = {NLM}, Pages = {980}, Pl = {United States}, Pmid = {14634627}, Pst = {ppublish}, Pt = {Letter}, Pubm = {Print}, Sb = {IM}, So = {Nat Struct Biol. 2003 Dec;10(12):980.}, Stat = {MEDLINE}, Title = {Announcing the worldwide {Protein Data Bank}.}, Volume = {10}, Year = {2003}}

@article{Berman:OMICS:2003, Affiliation = {Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, New Jersey 08854, USA. berman@rcsb.rutgers.edu}, Aid = {10.1089/153623103322006481 [doi]}, Au = {Berman HM and Westbrook J}, Author = {Berman, Helen M and Westbrook, John}, Da = {20030630}, Date-Added = {2006-07-06 01:35:29 -0400}, Date-Modified = {2006-07-06 01:35:29 -0400}, Dcom = {20030819}, Edat = {2003/07/02 05:00}, Ip = {1}, Jid = {101131135}, Journal = {OMICS}, Jt = {Omics : a journal of integrative biology.}, Keywords = {*Computational Biology, *Database Management Systems, *Dictionaries, *Vocabulary, Controlled}, Language = {eng}, Mhda = {2003/08/20 05:00}, Number = {1536-2310 (Print)}, Own = {NLM}, Pages = {9-10}, Pl = {United States}, Pmid = {12831545}, Pst = {ppublish}, Pt = {Journal Article}, Pubm = {Print}, Sb = {IM}, So = {OMICS. 2003 Spring;7(1):9-10.}, Stat = {MEDLINE}, Title = {The need for dictionaries, ontologies, and controlled vocabularies.}, Volume = {7}, Year = {2003}}

@article{Blumenthal:JAMA:1997, Affiliation = {Health Policy Research and Development Unit, Boston, MA 02114, USA.}, Au = {Blumenthal D and Campbell EG and Anderson MS and Causino N and Louis KS}, Author = {Blumenthal, D and Campbell, E G and Anderson, M S and Causino, N and Louis, K S}, Cin = {JAMA. 2001 May 2;285(17):2192-3; author reply 2193-5. PMID: 11325315}, Da = {19970428}, Date-Modified = {2006-07-06 00:55:35 -0400}, Dcom = {19970428}, Edat = {1997/04/16}, Gn = {KIE: Full author name: Louis, Karen Seashore}, Gr = {HG00724-01/HG/NHGRI}, Ip = {15}, Jid = {7501160}, Journal = {JAMA}, Jt = {JAMA : the journal of the American Medical Association.}, Keywords = {*Biological Sciences, *Biomedical Research, Contracts, Data Collection, *Faculty, Federal Government, Female, *Genetic Research, Humans, *Information Dissemination, *Intellectual Property, Logistic Models, Male, Multivariate Analysis, Patents, *Publishing, *Research, Research Support, Research Support, U.S. Gov't, P.H.S., Time Factors, United States, Universities}, Language = {eng}, Lr = {20041118}, Mhda = {1997/04/16 00:01}, Number = {0098-7484 (Print)}, Oid = {KIE: 54452}, Ot = {National Institutes of Health}, Oto = {KIE}, Own = {NLM}, Pages = {1224-8}, Pl = {UNITED STATES}, Pmid = {9103347}, Pst = {ppublish}, Pt = {Journal Article}, Pubm = {Print}, Sb = {IM}, So = {JAMA. 1997 Apr 16;277(15):1224-8.}, Stat = {MEDLINE}, Title = {Withholding research results in academic life science. {Evidence} from a national survey of faculty.}, Volume = {277}, Year = {1997}, Abstract = {OBJECTIVES: To identify the prevalence and determinants of data-withholding behaviors among academic life scientists. DESIGN: Mailed survey of 3394 life science faculty in the 50 universities that received the most funding from the National Institutes of Health in 1993. PARTICIPANTS: A total of 2167 faculty responded to the survey, a 64% response rate. OUTCOME MEASURES: Whether respondents delayed publication of their research results for more than 6 months and whether respondents refused to share research results with other university scientists in the last 3 years. RESULTS: A total of 410 respondents (19.8%) reported that publication of their research results had been delayed by more than 6 months at least once in the last 3 years to allow for patent application, to protect their scientific lead, to slow the dissemination of undesired results, to allow time to negotiate a patent, or to resolve disputes over the ownership of intellectual property. Also, 181 respondents (8.9%) reported refusing to share research results with other university scientists in the last 3 years. In multivariate analysis, participation in an academic-industry research relationship and engagement in the commercialization of university research were significantly associated with delays in publication. Odds ratios (ORs) and 95% confidence intervals (CIs) were 1.34 (1.07-1.59) and 3.15 (2.88-3.41), respectively. Variables associated with refusing to share results were conducting research similar to the Human Genome Project (OR, 2.09; 95% CI, 1.75-2.42), publication rate (OR, 1.02; 95% CI, 1.01-1.03), and engagement in commercialization of research (OR, 2.45; 95% CI, 2.08-2.82). CONCLUSIONS: Withholding of research results is not a widespread phenomenon among life-science researchers. However, withholding is more common among the most productive and entrepreneurial faculty. These results also suggest that data withholding has affected a significant number of life-science faculty and further study on data-withholding practices is suggested.}}

@article{Blumenthal:Acad-Med:2006, Affiliation = {Institute for Health Policy, Massachusetts General Hospital/Partners HealthCare System, 50 Staniford St., Boston, MA 02114, USA. dblumenthal@partners.org}, Aid = {81/2/137 [pii]}, Au = {Blumenthal D and Campbell EG and Gokhale M and Yucel R and Clarridge B and Hilgartner S and Holtzman NA}, Author = {Blumenthal, David and Campbell, Eric G and Gokhale, Manjusha and Yucel, Recai and Clarridge, Brian and Hilgartner, Stephen and Holtzman, Neil A}, Da = {20060126}, Dcom = {20060420}, Edat = {2006/01/27 09:00}, Gr = {1R01 HG 601789/HG/NHGRI}, Ip = {2}, Jid = {8904605}, Journal = {Acad Med}, Jt = {Academic medicine : journal of the Association of American Medical Colleges.}, Keywords = {*Access to Information, Adult, Biological Sciences/education/*statistics & numerical data, Biomedical Research/*trends, Comparative Study, Competitive Behavior, Confidentiality, Cooperative Behavior, Data Collection, *Faculty, Medical, Female, Genetics/education/*statistics & numerical data, Humans, *Interdisciplinary Communication, Male, Research Personnel/*psychology, Research Support, N.I.H., Extramural, United States, Universities}, Language = {eng}, Mhda = {2006/04/21 09:00}, Number = {1040-2446 (Print)}, Own = {NLM}, Pages = {137-45}, Pl = {United States}, Pmid = {16436574}, Pst = {ppublish}, Pt = {Journal Article}, Pubm = {Print}, Sb = {IM}, So = {Acad Med. 2006 Feb;81(2):137-45.}, Stat = {MEDLINE}, Title = {Data withholding in genetics and the other life sciences: prevalences and predictors.}, Volume = {81}, Year = {2006}, Abstract = {PURPOSE: To better understand the variety and prevalence of data withholding in genetics and the other life sciences and to explore factors associated with these behaviors. METHOD: In 2000, a sample of 2,893 geneticists and other life scientists (OLS) at the 100 most research-intensive universities in the United States were surveyed concerning data withholding and sharing. The instrument was developed and pretested in 1999. The two primary outcome measures were withholding in verbal exchanges with colleagues about unpublished research (verbal withholding) and withholding as part of the publishing process (publishing withholding). The independent variables related to the personal characteristics, research characteristics of faculty, and previous experience with data withholding. RESULTS: A total of 1,849 faculty responded (64\%): 1,240 geneticists and 600 OLS. Forty-four percent of geneticists and 32\% of OLS reported participating in any one of 13 forms of data withholding in the three previous years. Publishing withholding (geneticists 35\%, OLS 25\%) was more frequent than verbal withholding (geneticists 23\%, OLS 12\%). In multivariate analyses, male gender, participation in relationships with industry, mentors' discouraging data sharing, receipt of formal instruction in data sharing, and negative past experience with sharing were significantly associated with either verbal or publishing withholding among either geneticists or OLS. CONCLUSIONS: Data withholding is common in biomedical science, takes multiple forms, is influenced by a variety of characteristics of investigators and their training, and varies by field of science. Encouraging openness during the formative experiences of young investigators may be critical to increased data sharing, but the effects of formal training do not appear straightforward.}}

@article{Butler:Nature:2005, Aid = {10.1038/438548a [doi]}, Au = {Butler D}, Author = {Butler, Declan}, Da = {20051201}, Date-Added = {2006-07-06 01:30:33 -0400}, Date-Modified = {2006-07-06 01:30:36 -0400}, Dcom = {20051228}, Edat = {2005/12/02 09:00}, Ip = {7068}, Jid = {0410462}, Journal = {Nature}, Jt = {Nature.}, Keywords = {*Communication, Internet/*trends/*utilization, Peer Review, Research/trends, Publishing/trends, *Research Personnel/psychology/standards, Science/standards/*trends, Time Factors}, Language = {eng}, Mhda = {2005/12/29 09:00}, Number = {1476-4687 (Electronic)}, Own = {NLM}, Pages = {548-9}, Pl = {England}, Pmid = {16319855}, Pst = {ppublish}, Pt = {News}, Pubm = {Print}, Sb = {IM}, So = {Nature. 2005 Dec 1;438(7068):548-9.}, Stat = {MEDLINE}, Title = {Science in the web age: joint efforts.}, Volume = {438}, Year = {2005}}

@article{Campbell:JAMA:2002, Affiliation = {Institute for Health Policy, Massachusetts General Hospital, Boston, MA 02114, USA. ecampbell@partners.org}, Aid = {joc11433 [pii]}, Au = {Campbell EG and Clarridge BR and Gokhale M and Birenbaum L and Hilgartner S and Holtzman NA and Blumenthal D}, Author = {Campbell, Eric G and Clarridge, Brian R and Gokhale, Manjusha and Birenbaum, Lauren and Hilgartner, Stephen and Holtzman, Neil A and Blumenthal, David}, Cin = {JAMA. 2002 Apr 17;287(15):1939-40; author reply 1940. PMID: 11960533}, Da = {20020118}, Dcom = {20020204}, Edat = {2002/02/02 10:00}, Gn = {KIE: KIE Bib: genetic research}, Gr = {1R01HG01789-01/HG/NHGRI}, Ip = {4}, Jid = {7501160}, Journal = {JAMA}, Jt = {JAMA : the journal of the American Medical Association.}, Keywords = {Communication, *Data Collection, *Disclosure, *Ethics, Professional, *Genetic Research, *Genetics, Medical, Information Services, Intellectual Property, Interprofessional Relations, Research/*standards, Research Support, U.S. Gov't, P.H.S., United States, *Universities}, Language = {eng}, Lr = {20041118}, Mhda = {2002/02/05 10:01}, Number = {0098-7484 (Print)}, Oid = {KIE: 101724}, Ot = {Genetics and Reproduction}, Oto = {KIE}, Own = {NLM}, Pages = {473-80}, Pl = {United States}, Pmid = {11798369}, Pst = {ppublish}, Pt = {Journal Article}, Pubm = {Print}, Sb = {IM}, So = {JAMA. 2002 Jan 23-30;287(4):473-80.}, Stat = {MEDLINE}, Title = {Data withholding in academic genetics: evidence from a national survey.}, Volume = {287}, Year = {2002}, Abstract = {CONTEXT: The free and open sharing of information, data, and materials regarding published research is vital to the replication of published results, the efficient advancement of science, and the education of students. Yet in daily practice, the ideal of free sharing is often breached. OBJECTIVE: To understand the nature, extent, and consequences of data withholding in academic genetics. DESIGN, SETTING, AND PARTICIPANTS: Mailed survey (March-July 2000) of geneticists and other life scientists in the 100 US universities that received the most funding from the National Institutes of Health in 1998. Of a potential 3000 respondents, 2893 were eligible and 1849 responded, yielding an overall response rate of 64\%. We analyzed a subsample of 1240 self-identified geneticists and made a limited number of comparisons with 600 self-identified nongeneticists. MAIN OUTCOME MEASURES: Percentage of faculty who made requests for data that were denied; percentage of respondents who denied requests; influences on and consequences of withholding data; and changes over time in perceived willingness to share data. RESULTS: Forty-seven percent of geneticists who asked other faculty for additional information, data, or materials regarding published research reported that at least 1 of their requests had been denied in the preceding 3 years. Ten percent of all postpublication requests for additional information were denied. Because they were denied access to data, 28\% of geneticists reported that they had been unable to confirm published research. Twelve percent said that in the previous 3 years, they had denied another academician's request for data concerning published results. Among geneticists who said they had intentionally withheld data regarding their published work, 80\% reported that it required too much effort to produce the materials or information; 64\%, that they were protecting the ability of a graduate student, postdoctoral fellow, or junior faculty member to publish; and 53\%, that they were protecting their own ability to publish. Thirty-five percent of geneticists said that sharing had decreased during the last decade; 14\%, that sharing had increased. Geneticists were as likely as other life scientists to deny others' requests (odds ratio [OR], 1.39; 95\% confidence interval [CI], 0.81-2.40) and to have their own requests denied (OR, 0.97; 95\% CI, 0.69-1.40). However, other life scientists were less likely to report that withholding had a negative impact on their own research as well as their field of research. CONCLUSIONS: Data withholding occurs in academic genetics and it affects essential scientific activities such as the ability to confirm published results. Lack of resources and issues of scientific priority may play an important role in scientists' decisions to withhold data, materials, and information from other academic geneticists.}}

@article{10.1109/CSMR.2002.995808, Address = {Los Alamitos, CA, USA}, Author = {Arie Van Deursen and Eelco Visser}, Date-Modified = {2006-07-06 02:01:39 -0400}, Doi = {http://doi.ieeecomputersociety.org/10.1109/CSMR.2002.995808}, Isbn = {0-7695-1438-3}, Journal = , Pages = {0217}, Publisher = {IEEE Computer Society}, Title = , Volume = {00}, Year = {2002}}

@misc{Ecoliwiki, Author = , Note = {[Online; accessed 6-July-2006]}, Title = , Url = {http://ecoliwiki.net/colipedia/index.php?title=Main_Page&oldid=2269}, Year = {2006}}

@article{Giles:Nature:2005, Aid = {10.1038/438900a [doi]}, Au = {Giles J}, Author = {Giles, Jim}, Cin = {Nature. 2006 Feb 2;439(7076):534. PMID: 16452957}, Da = {20051215}, Date-Added = {2006-07-06 01:16:05 -0400}, Date-Modified = {2006-07-06 01:16:13 -0400}, Dcom = {20060111}, Edat = {2005/12/16 09:00}, Ip = {7070}, Jid = {0410462}, Journal = {Nature}, Jt = {Nature.}, Keywords = {Authorship, Comparative Study, *Encyclopedias, *Internet/trends, Publishing/*standards/*trends, Research Personnel}, Language = {eng}, Lr = {20060217}, Mhda = {2006/01/13 09:00}, Number = {1476-4687 (Electronic)}, Own = {NLM}, Pages = {900-1}, Pl = {England}, Pmid = {16355180}, Pst = {ppublish}, Pt = {News}, Pubm = {Print}, Sb = {IM}, So = {Nature. 2005 Dec 15;438(7070):900-1.}, Stat = {MEDLINE}, Title = {Internet encyclopaedias go head to head.}, Volume = {438}, Year = {2005}}

@article{Grumbling:Nucleic-Acids-Res:2006, Affiliation = {Department of Biology, Indiana University, 1001 E 3rd Street, Bloomington, IN 47405-7005, USA. ggrumbli@bio.indiana.edu}, Aid = {10.1093/nar/gkj068 [doi]}, Au = {Grumbling G and Strelets V}, Author = {Grumbling, Gary and Strelets, Victor}, Da = {20051229}, Date-Modified = {2006-07-06 00:53:07 -0400}, Dcom = {20060228}, Edat = {2005/12/31 09:00}, Gr = {P41-HG00739/HG/NHGRI}, Ip = {Database issue}, Jid = {0411011}, Journal = {Nucleic Acids Res}, Jt = {Nucleic acids research.}, Keywords = {Animals, Computer Graphics, *Databases, Genetic, Drosophila Proteins/genetics/physiology, Drosophila melanogaster/*anatomy & histology/*genetics/growth & development, Drosophilidae/genetics, Gene Expression, Genome, Insect, Genomics, Internet, Phenotype, Research Support, N.I.H., Extramural, Research Support, Non-U.S. Gov't, Systems Integration, User-Computer Interface, Vocabulary, Controlled}, Language = {eng}, Mhda = {2006/03/01 09:00}, Number = {1362-4962 (Electronic)}, Own = {NLM}, Pages = {D484-8}, Pl = {England}, Pmid = {16381917}, Pst = {ppublish}, Pt = {Journal Article}, Pubm = {Print}, Rn = {0 (Drosophila Proteins)}, Sb = {IM}, So = {Nucleic Acids Res. 2006 Jan 1;34(Database issue):D484-8.}, Stat = {MEDLINE}, Title = {{FlyBase}: anatomical data, images and queries.}, Volume = {34}, Year = {2006}, Abstract = {FlyBase (http://flybase.org/) is a database of genetic and genomic data on the model organism Drosophila melanogaster and the entire insect family Drosophilidae. The FlyBase Consortium curates, annotates, integrates and maintains a wide variety of data within this domain. Access to the data is provided through graphical and textual user interfaces tailored to particular types of data. FlyBase data types include maps at the cytological, genetic and sequence levels, genes and alleles including their products, functions, expression patterns, mutant phenotypes and genetic interactions as well as aberrant chromosomes, annotated genomes, genetic stock collections, transposons, transgene constructs and insertions, anatomy and images, bibliographic data, and community contact information.}}

@article{Jenssen:Drug-Discov-Today:2002, Affiliation = {Dept of Tumor Biology, Institute for Cancer Research, The Norwegian Radium Hospital, 0310 Oslo, Norway.}, Aid = {S1359644602024583 [pii]}, Au = {Jenssen TK and Hovig E}, Author = {Jenssen, Tor-Kristian and Hovig, Eivind}, Da = {20030127}, Date-Added = {2006-07-06 01:36:56 -0400}, Date-Modified = {2006-07-06 01:37:04 -0400}, Dcom = {20030221}, Edat = {2003/01/28 04:00}, Ip = {19}, Jid = {9604391}, Journal = {Drug Discov Today}, Jt = {Drug discovery today.}, Keywords = {Biology/*trends, Internet/*trends, *Semantics}, Language = {eng}, Mhda = {2003/02/22 04:00}, Number = {1359-6446 (Print)}, Own = {NLM}, Pages = {992}, Pl = {England}, Pmid = {12546914}, Pst = {ppublish}, Pt = {Letter}, Pubm = {Print}, Sb = {IM}, So = {Drug Discov Today. 2002 Oct 1;7(19):992.}, Stat = {MEDLINE}, Title = {The semantic web and biology.}, Volume = {7}, Year = {2002}}

@book{Leuf::2001, Author = {Bo Leuf and Ward Cunningham}, Date-Added = {2006-07-06 01:46:02 -0400}, Date-Modified = {2006-07-06 01:47:26 -0400}, Publisher = {Addison-Wesley Professional}, Title = {The Wiki Way: Collaboration and Sharing on the Internet}, Year = {2001}}

@misc{OWW:SBstarterkit, Author = , Note = {[Online; accessed 6-July-2006]}, Title = , Url = {http://openwetware.org/index.php?title=User:Nkuldell:SB_starter_kit&oldid=44459}, Year = {2006}}

@misc{OWW:BE.109collaboration, Author = , Note = {[Online; accessed 6-July-2006]}, Title = , Url = {http://openwetware.org/index.php?title=BE.109:DNA_engineering/DNA_engineering_by_PCR&action=history}, Year = {2006}}

@misc{OWW:BE.109studentcontribution, Author = , Note = {[Online; accessed 6-July-2006]}, Title = , Url = {http://openwetware.org/index.php?title=BE.109%3ADNA_engineering%2FAgarose_gel_electrophoresis&diff=20951&oldid=20911}, Year = {2006}}

@misc{OWW:Gettingstarted, Author = , Note = {[Online; accessed 6-July-2006]}, Title = , Url = {http://openwetware.org/index.php?title=OpenWetWare:Getting_started&oldid=40883}, Year = {2006}}

@misc{OWW:Labnotebook, Author = , Note = {[Online; accessed 6-July-2006]}, Title = , Url = {http://openwetware.org/index.php?title=User:Kalkao/notebook&oldid=47123}, Year = {2006}}

@misc{OWW:Steeringcommittee, Author = , Note = {[Online; accessed 6-July-2006]}, Title = , Url = {http://openwetware.org/index.php?title=OpenWetWare:Steering_committee&oldid=47155}, Year = {2006}}

@misc{OWW:TalkBE109Agarosegelelectrophoresis, Author = , Note = {[Online; accessed 6-July-2006]}, Title = , Url = {http://openwetware.org/index.php?title=Talk:BE.109:DNA_engineering/Agarose_gel_electrophoresis&oldid=21757}, Year = {2006}}

@misc{OWW:StudentNotes, Author = , Date-Modified = {2006-07-06 00:55:47 -0400}, Note = {[Online; accessed 6-July-2006]}, Title = , Url = {http://openwetware.org/index.php?title=User:Yeem/BE.180_notes/Semester_review&oldid=35942}, Year = {2006}}

@misc{OWW:BE109, Author = , Note = {[Online; accessed 6-July-2006]}, Title = , Url = {http://openwetware.org/index.php?title=BE.109&oldid=36681}, Year = {2006}}

@misc{OWW:Ecoligenotypes, Author = , Note = {[Online; accessed 6-July-2006]}, Title = , Url = {http://openwetware.org/index.php?title=E._coli_genotypes&oldid=47122}, Year = {2006}}

@misc{OWW:Victor3platereader, Author = , Note = {[Online; accessed 6-July-2006]}, Title = , Url = {http://openwetware.org/index.php?title=Endy:Victor3_plate_reader&oldid=46903}, Year = {2006}}

@misc{OWW:BetaGalactosidase, Author = , Note = {[Online; accessed 6-July-2006]}, Title = , Url = {http://openwetware.org/index.php?title=Beta-Galactosidase_Assay_%28A_better_Miller%29&oldid=15730}, Year = {2005}}

@misc{OWW:DNAligation, Author = , Note = {[Online; accessed 6-July-2006]}, Title = , Url = {http://openwetware.org/index.php?title=DNA_ligation&oldid=44446}, Year = {2006}}

@misc{OWW:TalkBE109Examineclones, Author = , Note = {[Online; accessed 6-July-2006]}, Title = , Url = {http://openwetware.org/index.php?title=Talk:BE.109:DNA_engineering/Examine_candidate_clones&oldid=23411}, Year = {2006}}

@article{Pearson:Nature:2006, Aid = {10.1038/441678a [doi]}, Au = {Pearson H}, Author = {Pearson, Helen}, Da = {20060608}, Date-Added = {2006-07-06 01:31:05 -0400}, Date-Modified = {2006-07-06 01:31:13 -0400}, Edat = {2006/06/09 09:00}, Ip = {7094}, Jid = {0410462}, Journal = {Nature}, Jt = {Nature.}, Language = {eng}, Mhda = {2006/06/09 09:00}, Number = {1476-4687 (Electronic)}, Own = {NLM}, Pages = {678}, Pl = {England}, Pmid = {16760944}, Pst = {ppublish}, Pt = {News}, Pubm = {Print}, Sb = {IM}, So = {Nature. 2006 Jun 8;441(7094):678.}, Stat = {In-Process}, Title = {Online methods share insider tricks.}, Volume = {441}, Year = {2006}}

@article{Schwarz:Nucleic-Acids-Res:2006, Affiliation = {Division of Biology, 156-29 California Institute of Technology, Pasadena, CA, 91125, USA. emsch@its.caltech.edu}, Aid = {10.1093/nar/gkj061 [doi]}, Au = {Schwarz EM and Antoshechkin I and Bastiani C and Bieri T and Blasiar D and Canaran P and Chan J and Chen N and Chen WJ and Davis P and Fiedler TJ and Girard L and Harris TW and Kenny EE and Kishore R and Lawson D and Lee R and Muller HM and Nakamura C and Ozersky P and Petcherski A and Rogers A and Spooner W and Tuli MA and Van Auken K and Wang D and Durbin R and Spieth J and Stein LD and Sternberg PW}, Author = {Schwarz, Erich M and Antoshechkin, Igor and Bastiani, Carol and Bieri, Tamberlyn and Blasiar, Darin and Canaran, Payan and Chan, Juancarlos and Chen, Nansheng and Chen, Wen J and Davis, Paul and Fiedler, Tristan J and Girard, Lisa and Harris, Todd W and Kenny, Eimear E and Kishore, Ranjana and Lawson, Dan and Lee, Raymond and Muller, Hans-Michael and Nakamura, Cecilia and Ozersky, Phil and Petcherski, Andrei and Rogers, Anthony and Spooner, Will and Tuli, Mary Ann and Van Auken, Kimberly and Wang, Daniel and Durbin, Richard and Spieth, John and Stein, Lincoln D and Sternberg, Paul W}, Da = {20051229}, Date-Modified = {2006-07-06 00:55:17 -0400}, Dcom = {20060228}, Edat = {2005/12/31 09:00}, Gr = {P41-HG02223/HG/NHGRI}, Ip = {Database issue}, Jid = {0411011}, Journal = {Nucleic Acids Res}, Jt = {Nucleic acids research.}, Keywords = {Animals, Caenorhabditis elegans/*genetics/physiology, Caenorhabditis elegans Proteins/*chemistry/*genetics, DNA, Complementary/chemistry, *Databases, Genetic, Expressed Sequence Tags/chemistry, Genome, Helminth, Genomics, Internet, Polymorphism, Single Nucleotide, RNA Interference, Research Support, N.I.H., Extramural, Research Support, Non-U.S. Gov't, *Software, User-Computer Interface}, Language = {eng}, Mhda = {2006/03/01 09:00}, Number = {1362-4962 (Electronic)}, Own = {NLM}, Pages = {D475-8}, Pl = {England}, Pmid = {16381915}, Pst = {ppublish}, Pt = {Journal Article}, Pubm = {Print}, Rn = {0 (DNA, Complementary)}, Sb = {IM}, So = {Nucleic Acids Res. 2006 Jan 1;34(Database issue):D475-8.}, Stat = {MEDLINE}, Title = {{WormBase}: better software, richer content.}, Volume = {34}, Year = {2006}, Abstract = {WormBase (http://wormbase.org), the public database for genomics and biology of Caenorhabditis elegans, has been restructured for stronger performance and expanded for richer biological content. Performance was improved by accelerating the loading of central data pages such as the omnibus Gene page, by rationalizing internal data structures and software for greater portability, and by making the Genome Browser highly customizable in how it views and exports genomic subsequences. Arbitrarily complex, user-specified queries are now possible through Textpresso (for all available literature) and through WormMart (for most genomic data). Biological content was enriched by reconciling all available cDNA and expressed sequence tag data with gene predictions, clarifying single nucleotide polymorphism and RNAi sites, and summarizing known functions for most genes studied in this organism.}}

@article{Tonkin:Ariadne:2005, Author = {Emma Tonkin}, Date-Added = {2006-07-06 01:49:25 -0400}, Date-Modified = {2006-07-06 01:50:47 -0400}, Journal = {Ariadne}, Title = {Making the Case for a Wiki}, Url = {http://www.ariadne.ac.uk/issue42/tonkin/}, Volume = {42}, Year = {2005}}

@article{Vogeli:Acad-Med:2006, Affiliation = {Institute for Health Policy, 50 Staniford Street (9th floor), Boston, MA 02114, USA.}, Aid = {81/2/128 [pii]}, Au = {Vogeli C and Yucel R and Bendavid E and Jones LM and Anderson MS and Louis KS and Campbell EG}, Author = {Vogeli, Christine and Yucel, Recai and Bendavid, Eran and Jones, Lisa M and Anderson, Melissa S and Louis, Karen Seashore and Campbell, Eric G}, Da = {20060126}, Dcom = {20060420}, Edat = {2006/01/27 09:00}, Ip = {2}, Jid = {8904605}, Journal = {Acad Med}, Jt = {Academic medicine : journal of the Association of American Medical Colleges.}, Keywords = {*Access to Information, Adult, Biological Sciences/*education, Chemical Engineering/*education, Comparative Study, Competitive Behavior, Cooperative Behavior, Data Collection, Education, Graduate, Efficiency, Ethnic Groups, Female, Humans, Informatics/*education, *Interdisciplinary Communication, Male, *Research Personnel/psychology, Research Support/classification/*statistics & numerical data, Research Support, N.I.H., Extramural, United States, Universities}, Language = {eng}, Mhda = {2006/04/21 09:00}, Number = {1040-2446 (Print)}, Own = {NLM}, Pages = {128-36}, Pl = {United States}, Pmid = {16436573}, Pst = {ppublish}, Pt = {Journal Article}, Pubm = {Print}, Sb = {IM}, So = {Acad Med. 2006 Feb;81(2):128-36.}, Stat = {MEDLINE}, Title = {Data withholding and the next generation of scientists: results of a national survey.}, Volume = {81}, Year = {2006}, Abstract = {PURPOSE: To provide the first national data on the nature, extent, and consequences of withholding among life science trainees. METHOD: In 2003, the authors surveyed 1,077 second-year doctoral students and postdoctoral fellows in life sciences at 50 U.S. universities, with a comparison group of trainees in computer science and chemical engineering. The study variables examined trainees' exposure to and the consequences of data withholding. RESULTS: Two hundred forty-six trainees (23.0\%) reported that they had asked for and been denied access to information, data, materials, or programming associated with published research and 221 (20.6\%) to unpublished research. Eighty-five trainees (7.9\%) reported that they had denied another academic scientist's request(s) related to their own published research. Five hundred thirty-three trainees (50.8\%) reported that withholding had had a negative effect on the progress of their research, 508 (48.5\%) on the rate of discovery in their lab/research group, 472 (45.0\%) on the quality of their relationships with academic scientists, 346 (33.0\%) on the quality of their education, and 299 (28.5\%) on the level of communication in their lab/research group. Trainees denied access to research were significantly more likely to report that data withholding had had a negative effect on several aspects of the educational experience. CONCLUSIONS: Data withholding had demonstrated negative effects on trainees. The life sciences, more so than chemical engineering or computer science, will have to address this issue among its trainees. Failure to do so could result in delayed research, inefficient training, and a culture of withholding among future life scientists.}}

@article{10.1109/ITCC.2004.1286462, Address = {Los Alamitos, CA, USA}, Author = {Chien-min Wang and David Turner}, Doi = {http://doi.ieeecomputersociety.org/10.1109/ITCC.2004.1286462}, Isbn = {0-7695-2108-8}, Journal = , Pages = {255}, Publisher = {IEEE Computer Society}, Title = , Volume = {01}, Year = {2004}}

@article{Wheeler:Nucleic-Acids-Res:2003, Affiliation = {National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Building 38A, 8600 Rockville Pike, Bethesda, MD 20894, USA. wheeler@ncbi.nlm.nih.gov}, Au = {Wheeler DL and Church DM and Federhen S and Lash AE and Madden TL and Pontius JU and Schuler GD and Schriml LM and Sequeira E and Tatusova TA and Wagner L}, Author = {Wheeler, David L and Church, Deanna M and Federhen, Scott and Lash, Alex E and Madden, Thomas L and Pontius, Joan U and Schuler, Gregory D and Schriml, Lynn M and Sequeira, Edwin and Tatusova, Tatiana A and Wagner, Lukas}, Da = {20030109}, Date-Modified = {2006-07-06 01:00:09 -0400}, Dcom = {20030314}, Edat = {2003/01/10 04:00}, Ip = {1}, Jid = {0411011}, Journal = {Nucleic Acids Res}, Jt = {Nucleic acids research.}, Keywords = {Animals, *Biotechnology, Chromosome Mapping, *Databases, Genetic, Gene Expression Profiling, Genes, Genome, Humans, Information Storage and Retrieval, Mice, Models, Molecular, Phenotype, Protein Structure, Tertiary, Sequence Alignment/methods, Sequence Homology, United States}, Language = {eng}, Lr = {20041117}, Mhda = {2003/03/15 04:00}, Number = {1362-4962 (Electronic)}, Own = {NLM}, Pages = {28-33}, Pl = {England}, Pmid = {12519941}, Pst = {ppublish}, Pt = {Journal Article}, Pubm = {Print}, Sb = {IM}, So = {Nucleic Acids Res. 2003 Jan 1;31(1):28-33.}, Stat = {MEDLINE}, Title = {Database resources of the {National Center for Biotechnology}.}, Volume = {31}, Year = {2003}, Abstract = {In addition to maintaining the GenBank(R) nucleic acid sequence database, the National Center for Biotechnology Information (NCBI) provides data analysis and retrieval resources for the data in GenBank and other biological data made available through NCBI's Web site. NCBI resources include Entrez, PubMed, PubMed Central (PMC), LocusLink, the NCBITaxonomy Browser, BLAST, BLAST Link (BLink), Electronic PCR (e-PCR), Open Reading Frame (ORF) Finder, References Sequence (RefSeq), UniGene, HomoloGene, ProtEST, Database of Single Nucleotide Polymorphisms (dbSNP), Human/Mouse Homology Map, Cancer Chromosome Aberration Project (CCAP), Entrez Genomes and related tools, the Map Viewer, Model Maker (MM), Evidence Viewer (EV), Clusters of Orthologous Groups (COGs) database, Retroviral Genotyping Tools, SAGEmap, Gene Expression Omnibus (GEO), Online Mendelian Inheritance in Man (OMIM), the Molecular Modeling Database (MMDB), the Conserved Domain Database (CDD), and the Conserved Domain Architecture Retrieval Tool (CDART). Augmenting many of the Web applications are custom implementations of the BLAST program optimized to search specialized data sets. All of the resources can be accessed through the NCBI home page at: http://www.ncbi.nlm.nih.gov.}}

@misc{SemanticMediaWiki, Author = , Note = {[Online; accessed 6-July-2006]}, Title = , Url = {http://meta.wikimedia.org/w/index.php?title=Semantic_MediaWiki&oldid=385893}, Year = {2006}}

@inproceedings{Wolstencroft:ISWC:2005, Author = {Katherine Wolstencroft and Andy Brass and Ian Horrocks and Phil Lord and Ulrike Sattler and Robert Stevens and Daniele Turi}, Booktitle = {Proc.\ of the 2006 International Semantic Web Conference (ISWC 2006)}, Date-Modified = {2006-07-06 01:44:45 -0400}, Note = {To appear}, Publisher = {Springer}, Series = {Lecture Notes in Artificial Intelligence}, Title = {A Little Semantic Web Goes a Long Way in Biology}, Url = {http://www.cs.man.ac.uk/~horrocks/Publications/download/2005/WBHL05.pdf}, Year = 2005}

@article{Yager:Nature:2006, Aid = {10.1038/440278a [doi]}, Au = {Yager K}, Author = {Yager, Kevin}, Con = {Nature. 2006 Feb 2;439(7076):516-7. PMID: 16452941}, Da = {20060316}, Date-Added = {2006-07-06 01:22:04 -0400}, Date-Modified = {2006-07-06 01:22:11 -0400}, Dcom = {20060411}, Edat = {2006/03/17 09:00}, Ip = {7082}, Jid = {0410462}, Journal = {Nature}, Jt = {Nature.}, Keywords = {*Encyclopedias, Internet/*standards/*trends, Science/methods/*standards, Software}, Language = {eng}, Mhda = {2006/04/12 09:00}, Number = {1476-4687 (Electronic)}, Own = {NLM}, Pages = {278}, Pl = {England}, Pmid = {16541049}, Pst = {ppublish}, Pt = {Letter}, Pubm = {Print}, Sb = {IM}, So = {Nature. 2006 Mar 16;440(7082):278.}, Stat = {MEDLINE}, Title = {Wiki ware could harness the Internet for science.}, Volume = {440}, Year = {2006}}

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