-
1
-
-
79954533893
-
PubMed and beyond: a survey of web tools for searching biomedical literature
-
Lu Z. PubMed and beyond: a survey of web tools for searching biomedical literature. Database the journal of biological databases and curation 2011, 2011:13.
-
(2011)
Database the journal of biological databases and curation
, vol.2011
, pp. 13
-
-
Lu, Z.1
-
2
-
-
2042437650
-
Initial sequencing and analysis of the human genome
-
10.1038/35057062, 11237011
-
Lander ES, Linton LM, Birren B, Nusbaum C, Zody MC, Baldwin J, Devon K, Dewar K, Doyle M, FitzHugh W, Funke R, Gage D, Harris K, Heaford A, Howland J, Kann L, Lehoczky J, LeVine R, McEwan P, McKernan K, Meldrim J, Mesirov JP, Miranda C, Morris W, Naylor J, Raymond C, Rosetti M, Santos R, Sheridan A, Sougnez C, et al. Initial sequencing and analysis of the human genome. Nature 2001, 409:860-921. 10.1038/35057062, 11237011.
-
(2001)
Nature
, vol.409
, pp. 860-921
-
-
Lander, E.S.1
Linton, L.M.2
Birren, B.3
Nusbaum, C.4
Zody, M.C.5
Baldwin, J.6
Devon, K.7
Dewar, K.8
Doyle, M.9
FitzHugh, W.10
Funke, R.11
Gage, D.12
Harris, K.13
Heaford, A.14
Howland, J.15
Kann, L.16
Lehoczky, J.17
LeVine, R.18
McEwan, P.19
McKernan, K.20
Meldrim, J.21
Mesirov, J.P.22
Miranda, C.23
Morris, W.24
Naylor, J.25
Raymond, C.26
Rosetti, M.27
Santos, R.28
Sheridan, A.29
Sougnez, C.30
more..
-
3
-
-
0035895505
-
The sequence of the human genome
-
Venter JC, Adams MD, Myers EW, Li PW, Mural RJ, Sutton GG, Smith HO, Yandell M, Evans CA, Holt RA, Gocayne JD, Amanatides P, Ballew RM, Huson DH, Wortman JR, Zhang Q, Kodira CD, Zheng XH, Chen L, Skupski M, Subramanian G, Thomas PD, Zhang J, Gabor Miklos GL, Nelson C, Broder S, Clark AG, Nadeau J, McKusick VA, Zinder N, et al. The sequence of the human genome. Science (New York, NY) 2001, 291:1304-1351.
-
(2001)
Science (New York, NY)
, vol.291
, pp. 1304-1351
-
-
Venter, J.C.1
Adams, M.D.2
Myers, E.W.3
Li, P.W.4
Mural, R.J.5
Sutton, G.G.6
Smith, H.O.7
Yandell, M.8
Evans, C.A.9
Holt, R.A.10
Gocayne, J.D.11
Amanatides, P.12
Ballew, R.M.13
Huson, D.H.14
Wortman, J.R.15
Zhang, Q.16
Kodira, C.D.17
Zheng, X.H.18
Chen, L.19
Skupski, M.20
Subramanian, G.21
Thomas, P.D.22
Zhang, J.23
Gabor Miklos, G.L.24
Nelson, C.25
Broder, S.26
Clark, A.G.27
Nadeau, J.28
McKusick, V.A.29
Zinder, N.30
more..
-
4
-
-
0034069495
-
Gene Ontology: tool for the unification of biology
-
10.1038/75556, 3037419, 10802651
-
Ashburner M, Ball C, Blake J, Botstein D, Butler H, Cherry JM, Davis A, Dolinski K, Dwight S, Eppig J, Harris M, Hill D, Issel-Tarver L, Kasarskis A, Lewis S, Matese J, Richardson J, Ringwald M, Rubin G, Sherlock G. Gene Ontology: tool for the unification of biology. Nat Genet 2000, 25:25-29. 10.1038/75556, 3037419, 10802651.
-
(2000)
Nat Genet
, vol.25
, pp. 25-29
-
-
Ashburner, M.1
Ball, C.2
Blake, J.3
Botstein, D.4
Butler, H.5
Cherry, J.M.6
Davis, A.7
Dolinski, K.8
Dwight, S.9
Eppig, J.10
Harris, M.11
Hill, D.12
Issel-Tarver, L.13
Kasarskis, A.14
Lewis, S.15
Matese, J.16
Richardson, J.17
Ringwald, M.18
Rubin, G.19
Sherlock, G.20
more..
-
5
-
-
27344435774
-
Gene set enrichment analysis: a knowledge-based approach for interpreting genome-wide expression profiles
-
10.1073/pnas.0506580102, 1239896, 16199517
-
Subramanian A, Tamayo P, Mootha VK, Mukherjee S, Ebert BL, Gillette MA, Paulovich A, Pomeroy SL, Golub TR, Lander ES, Mesirov JP. Gene set enrichment analysis: a knowledge-based approach for interpreting genome-wide expression profiles. Proceedings of the National Academy of Sciences of the United States of America 2005, 102:15545-15550. 10.1073/pnas.0506580102, 1239896, 16199517.
-
(2005)
Proceedings of the National Academy of Sciences of the United States of America
, vol.102
, pp. 15545-15550
-
-
Subramanian, A.1
Tamayo, P.2
Mootha, V.K.3
Mukherjee, S.4
Ebert, B.L.5
Gillette, M.A.6
Paulovich, A.7
Pomeroy, S.L.8
Golub, T.R.9
Lander, E.S.10
Mesirov, J.P.11
-
6
-
-
58549112996
-
Bioinformatics enrichment tools: paths toward the comprehensive functional analysis of large gene lists
-
10.1093/nar/gkn923, 2615629, 19033363
-
Huang DW, Sherman BT, Lempicki RA. Bioinformatics enrichment tools: paths toward the comprehensive functional analysis of large gene lists. Nucleic Acids Research 2009, 37:1-13. 10.1093/nar/gkn923, 2615629, 19033363.
-
(2009)
Nucleic Acids Research
, vol.37
, pp. 1-13
-
-
Huang, D.W.1
Sherman, B.T.2
Lempicki, R.A.3
-
7
-
-
34547844156
-
Manual curation is not sufficient for annotation of genomic databases
-
Baumgartner W, Cohen B, Fox L, Acquaah-Mensah G, Hunter L. Manual curation is not sufficient for annotation of genomic databases. Bioinformatics (Oxford, England) 2007, 23(13):i41-48.
-
(2007)
Bioinformatics (Oxford, England)
, vol.23
, Issue.13
-
-
Baumgartner, W.1
Cohen, B.2
Fox, L.3
Acquaah-Mensah, G.4
Hunter, L.5
-
8
-
-
51349168137
-
Big data: Wikiomics
-
10.1038/455022a, 18769412
-
Waldrop M. Big data: Wikiomics. Nature 2008, 455:22-25. 10.1038/455022a, 18769412.
-
(2008)
Nature
, vol.455
, pp. 22-25
-
-
Waldrop, M.1
-
9
-
-
78549238900
-
No rest for the bio-wikis
-
10.1038/468359a
-
Callaway E. No rest for the bio-wikis. Nature 2010, 10.1038/468359a.
-
(2010)
Nature
-
-
Callaway, E.1
-
10
-
-
48349115184
-
A gene wiki for community annotation of gene function
-
10.1371/journal.pbio.0060175, 2443188, 18613750
-
Huss JW, Orozco C, Goodale J, Wu C, Batalov S, Vickers TJ, Valafar F, Su AI. A gene wiki for community annotation of gene function. PLoS biology 2008, 6:e175. 10.1371/journal.pbio.0060175, 2443188, 18613750.
-
(2008)
PLoS biology
, vol.6
-
-
Huss, J.W.1
Orozco, C.2
Goodale, J.3
Wu, C.4
Batalov, S.5
Vickers, T.J.6
Valafar, F.7
Su, A.I.8
-
11
-
-
75549087395
-
The Gene Wiki: community intelligence applied to human gene annotation
-
10.1093/nar/gkp760, 2808918, 19755503
-
Huss JW, Lindenbaum P, Martone M, Roberts D, Pizarro A, Valafar F, Hogenesch JB, Su AI. The Gene Wiki: community intelligence applied to human gene annotation. Nucleic acids research 2010, 38:D633-639. 10.1093/nar/gkp760, 2808918, 19755503.
-
(2010)
Nucleic acids research
, vol.38
-
-
Huss, J.W.1
Lindenbaum, P.2
Martone, M.3
Roberts, D.4
Pizarro, A.5
Valafar, F.6
Hogenesch, J.B.7
Su, A.I.8
-
12
-
-
50449088836
-
A wiki for the life sciences where authorship matters
-
10.1038/ng.f.217, 18728691
-
Hoffmann R. A wiki for the life sciences where authorship matters. Nature genetics 2008, 40:1047-1051. 10.1038/ng.f.217, 18728691.
-
(2008)
Nature genetics
, vol.40
, pp. 1047-1051
-
-
Hoffmann, R.1
-
13
-
-
47149084410
-
Calling on a million minds for community annotation in WikiProteins
-
10.1186/gb-2008-9-5-r89, 2441475, 18507872
-
Mons B, Ashburner M, Chichester C, van Mulligen E, Weeber M, den Dunnen J, van Ommen G-J, Musen M, Cockerill M, Hermjakob H, Mons A, Packer A, Pacheco R, Lewis S, Berkeley A, Melton W, Barris N, Wales J, Meijssen G, Moeller E, Roes PJ, Borner K, Bairoch A. Calling on a million minds for community annotation in WikiProteins. Genome biology 2008, 9:R89. 10.1186/gb-2008-9-5-r89, 2441475, 18507872.
-
(2008)
Genome biology
, vol.9
-
-
Mons, B.1
Ashburner, M.2
Chichester, C.3
van Mulligen, E.4
Weeber, M.5
den Dunnen, J.6
van Ommen, G.-J.7
Musen, M.8
Cockerill, M.9
Hermjakob, H.10
Mons, A.11
Packer, A.12
Pacheco, R.13
Lewis, S.14
Berkeley, A.15
Melton, W.16
Barris, N.17
Wales, J.18
Meijssen, G.19
Moeller, E.20
Roes, P.J.21
Borner, K.22
Bairoch, A.23
more..
-
14
-
-
77955542170
-
TOPSAN: a collaborative annotation environment for structural genomics
-
10.1186/1471-2105-11-426, 2936398, 20716366
-
Weekes D, Krishna SS, Bakolitsa C, Wilson IA, Godzik A, Wooley J. TOPSAN: a collaborative annotation environment for structural genomics. BMC Bioinformatics 2010, 11:426. 10.1186/1471-2105-11-426, 2936398, 20716366.
-
(2010)
BMC Bioinformatics
, vol.11
, pp. 426
-
-
Weekes, D.1
Krishna, S.S.2
Bakolitsa, C.3
Wilson, I.A.4
Godzik, A.5
Wooley, J.6
-
15
-
-
77956545718
-
PDBWiki: added value through community annotation of the Protein Data Bank
-
Stehr H, Duarte JM, Lappe M, Bhak J, Bolser DM. PDBWiki: added value through community annotation of the Protein Data Bank. Database the journal of biological databases and curation 2010, 2010:8.
-
(2010)
Database the journal of biological databases and curation
, vol.2010
, pp. 8
-
-
Stehr, H.1
Duarte, J.M.2
Lappe, M.3
Bhak, J.4
Bolser, D.M.5
-
16
-
-
84856487835
-
SNPedia
-
SNPedia. , http://www.snpedia.com
-
-
-
-
17
-
-
48349105261
-
WikiPathways: pathway editing for the people
-
10.1371/journal.pbio.0060184, 2475545, 18651794
-
Pico AR, Kelder T, van Iersel MP, Hanspers K, Conklin BR, Evelo C. WikiPathways: pathway editing for the people. PLoS biology 2008, 6:e184. 10.1371/journal.pbio.0060184, 2475545, 18651794.
-
(2008)
PLoS biology
, vol.6
-
-
Pico, A.R.1
Kelder, T.2
van Iersel, M.P.3
Hanspers, K.4
Conklin, B.R.5
Evelo, C.6
-
18
-
-
84908087962
-
A community-curated consensual annotation that is continuously updated: the Bacillus subtilis centred wiki SubtiWiki
-
Flórez LA, Roppel SF, Schmeisky AG, Lammers CR, Stülke J. A community-curated consensual annotation that is continuously updated: the Bacillus subtilis centred wiki SubtiWiki. Database 2009, 2009:9.
-
(2009)
Database
, vol.2009
, pp. 9
-
-
Flórez, L.A.1
Roppel, S.F.2
Schmeisky, A.G.3
Lammers, C.R.4
Stülke, J.5
-
19
-
-
77954506225
-
The Open Biomedical Annotator
-
Jonquet C, Shah NH, Musen MA, Ontology B. The Open Biomedical Annotator. AMIA Summit on Translational Bioinformatics 2009, 2009:56-60.
-
(2009)
AMIA Summit on Translational Bioinformatics
, vol.2009
, pp. 56-60
-
-
Jonquet, C.1
Shah, N.H.2
Musen, M.A.3
Ontology, B.4
-
20
-
-
0035752429
-
Effective mapping of biomedical text to the UMLS Metathesaurus: the MetaMap program
-
Philadelphia: Hanley & Belfus
-
Aronson AR. Effective mapping of biomedical text to the UMLS Metathesaurus: the MetaMap program. American Medical Informatics Annual Symposium 2001, 17-21. Philadelphia: Hanley & Belfus.
-
(2001)
American Medical Informatics Annual Symposium
, pp. 17-21
-
-
Aronson, A.R.1
-
21
-
-
66349110163
-
Annotating the human genome with Disease Ontology
-
Osborne J, Flatow J, Holko M, Lin S, Kibbe W, Zhu L, Danila M, Feng G, Chisholm R. Annotating the human genome with Disease Ontology. BMC Genomics 2009, 10.
-
(2009)
BMC Genomics
, pp. 10
-
-
Osborne, J.1
Flatow, J.2
Holko, M.3
Lin, S.4
Kibbe, W.5
Zhu, L.6
Danila, M.7
Feng, G.8
Chisholm, R.9
-
22
-
-
0037294313
-
The Gene Ontology Annotation (GOA) Project-Application of GO in SWISS-PROT, TrEMBL and InterPro
-
10.1002/cfg.235, 2447390, 18629103
-
Camon E, Barrell D, Brooksbank C, Magrane M, Apweiler R. The Gene Ontology Annotation (GOA) Project-Application of GO in SWISS-PROT, TrEMBL and InterPro. Comparative and Functional Genomics 2003, 4:71-74. 10.1002/cfg.235, 2447390, 18629103.
-
(2003)
Comparative and Functional Genomics
, vol.4
, pp. 71-74
-
-
Camon, E.1
Barrell, D.2
Brooksbank, C.3
Magrane, M.4
Apweiler, R.5
-
23
-
-
34547771661
-
Automatic extraction of gene ontology annotation and its correlation with clusters in protein networks
-
Daraselia N, Yuryev A, Egorov S, Mazo I, Ispolatov I. Automatic extraction of gene ontology annotation and its correlation with clusters in protein networks. BMC Bioinformatics 2007, 8.
-
(2007)
BMC Bioinformatics
, vol.8
-
-
Daraselia, N.1
Yuryev, A.2
Egorov, S.3
Mazo, I.4
Ispolatov, I.5
-
24
-
-
84856465033
-
OR2F1
-
OR2F1. , http://en.wikipedia.org/wiki/OR2F1
-
-
-
-
25
-
-
84856478167
-
Osteopontin
-
Osteopontin. , http://en.wikipedia.org/wiki/Osteopontin
-
-
-
-
26
-
-
84983060347
-
An ontology-neutral framework for enrichment analysis
-
3041299, 21347088
-
Tirrell R, Evani U, Berman AE, Mooney SD, Musen MA, Shah NH. An ontology-neutral framework for enrichment analysis. AMIA Annual Symposium proceedings/AMIA Symposium AMIA Symposium 2010, 2010:797-801. 3041299, 21347088.
-
(2010)
AMIA Annual Symposium proceedings/AMIA Symposium AMIA Symposium
, vol.2010
, pp. 797-801
-
-
Tirrell, R.1
Evani, U.2
Berman, A.E.3
Mooney, S.D.4
Musen, M.A.5
Shah, N.H.6
-
27
-
-
83755218842
-
Enabling enrichment analysis with the Human Disease Ontology
-
Available online 29 April, 2011, 10.1016/j.jbi.2011.04.007
-
Lependu P, Musen MA, Shah NH. Enabling enrichment analysis with the Human Disease Ontology. Journal of Biomedical Informatics Available online 29 April, 2011, 10.1016/j.jbi.2011.04.007.
-
Journal of Biomedical Informatics
-
-
Lependu, P.1
Musen, M.A.2
Shah, N.H.3
-
28
-
-
70349881426
-
Comparison of concept recognizers for building the Open Biomedical Annotator
-
10.1186/1471-2105-10-S9-S14, 2762063, 19828074
-
Shah NH, Bhatia N, Jonquet C, Rubin D, Chiang AP, Musen MA. Comparison of concept recognizers for building the Open Biomedical Annotator. BMC Bioinformatics 2009, 10(Suppl 9):S14. 10.1186/1471-2105-10-S9-S14, 2762063, 19828074.
-
(2009)
BMC Bioinformatics
, vol.10
, Issue.SUPPL. 9
-
-
Shah, N.H.1
Bhatia, N.2
Jonquet, C.3
Rubin, D.4
Chiang, A.P.5
Musen, M.A.6
-
29
-
-
33947304181
-
Overview of BioCreAtIvE: critical assessment of information extraction for biology
-
Hirschman L, Yeh A, Blaschke C, Valencia A. Overview of BioCreAtIvE: critical assessment of information extraction for biology. BMC bioinformatics [electronic resource] 2005, 6(Suppl 1):S1.
-
(2005)
BMC bioinformatics [electronic resource]
, vol.6
, Issue.SUPPL. 1
-
-
Hirschman, L.1
Yeh, A.2
Blaschke, C.3
Valencia, A.4
-
30
-
-
33947311528
-
An evaluation of GO annotation retrieval for BioCreAtIvE and GOA
-
1866391, 16351743
-
Camon EB, Barrell DG, Dimmer EC, Lee V, Magrane M, Maslen J, Binns D, Apweiler R. An evaluation of GO annotation retrieval for BioCreAtIvE and GOA. BMC Bioinformatics 2005, 6:S17. 1866391, 16351743.
-
(2005)
BMC Bioinformatics
, vol.6
-
-
Camon, E.B.1
Barrell, D.G.2
Dimmer, E.C.3
Lee, V.4
Magrane, M.5
Maslen, J.6
Binns, D.7
Apweiler, R.8
-
31
-
-
58149375832
-
Facts from text: can text mining help to scale-up high-quality manual curation of gene products with ontologies?
-
10.1093/bib/bbn043, 19060303
-
Winnenburg R, Wächter T, Plake C, Doms A, Schroeder M. Facts from text: can text mining help to scale-up high-quality manual curation of gene products with ontologies?. Briefings in Bioinformatics 2008, 9:466-478. 10.1093/bib/bbn043, 19060303.
-
(2008)
Briefings in Bioinformatics
, vol.9
, pp. 466-478
-
-
Winnenburg, R.1
Wächter, T.2
Plake, C.3
Doms, A.4
Schroeder, M.5
-
33
-
-
84856558362
-
Wikipedia API
-
Wikipedia API. , http://en.wikipedia.org/w/api.php
-
-
-
-
34
-
-
84856478169
-
NCBO Annotator Web Service Documentation
-
NCBO Annotator Web Service Documentation. , http://www.bioontology.org/wiki/index.php/Annotator_Web_service
-
-
-
-
35
-
-
84856449965
-
GO Ontology Structure
-
GO Ontology Structure. , http://www.geneontology.org/GO.ontology.structure.shtml
-
-
-
-
37
-
-
84856465034
-
Gene Wiki Code Repository
-
Gene Wiki Code Repository. , http://code.google.com/p/genewiki/
-
-
-
-
38
-
-
33847264343
-
Enrichment or depletion of a GO category within a class of genes: which test?
-
10.1093/bioinformatics/btl633, 17182697
-
Rivals I, Personnaz L, Taing L, Potier MC. Enrichment or depletion of a GO category within a class of genes: which test?. Bioinformatics 2007, 23(4):401-407. 10.1093/bioinformatics/btl633, 17182697.
-
(2007)
Bioinformatics
, vol.23
, Issue.4
, pp. 401-407
-
-
Rivals, I.1
Personnaz, L.2
Taing, L.3
Potier, M.C.4
|