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DATABASES

NCBI

We used data found in NCBI for gene and protein annotations in SOURCE.

Reference:


Wheeler DL, Chappey C, Lash AE, Leipe DD, Madden TL, Schuler GD, Tatusova TA, Rapp BA.
Database resources of the National Center for Biotechnology Information.
Nucleic Acids Res. 2000 Jan 1;28(1):10-4. [PubMed] [PDF]


Benson DA, Karsch-Mizrachi I, Lipman DJ, Ostell J, Rapp BA, Wheeler DL (2000).
GenBank.
Nucleic Acids Res 2000 Jan 1;28(1):15-18. [PubMed] [PDF]

GeneCards

We used data found in Genecards for gene synonyms in SOURCE.

Reference:


Rebhan, M., Chalifa-Caspi, V., Prilusky, J., Lancet, D.
GeneCards: A novel functional genomics compendium with automated data mining and query reformulation support.
Bioinformatics: 14:656-664 (1998). [PDF] [PubMed]


Rebhan, M., Chalifa-Caspi, V., Prilusky, J., Lancet, D.
GeneCards: integrating information about genes, proteins and diseases.
Trends in Genetics 13: 163 (1997). [PubMed] [PDF]

LocusLink

We used data found in LocusLink for gene and protein annotations in SOURCE.
Reference:

Pruitt KD, Maglott DR
RefSeq and LocusLink: NCBI gene-centered resources.
Nucleic Acids Res 2001 Jan 1;29(1):137-140 [PubMed] [PDF file]


Introducing RefSeq and LocusLink: curated human genome resources at the NCBI.
Pruitt KD, Katz KS, Sicotte H, Maglott DR
Trends Genet. 2000 Jan;16(1):44-47. [PDF] [ Pubmed]

rhDB

We used data found in RHdb for gene and protein annotations in SOURCE.
Reference:

The Radiation Hybrid Database
Patricia Rodriguez-Tome and Philip Lijnzaad
Nucleic Acids Research 25(1):81-84(1997). [PDF] [PubMed]


RHdb: the Radiation Hybrid Database
Patricia Rodriguez-Tome and Philip Lijnzaad
Nucleic Acids Research 29(1):165-166 (2001). [PDF] [PubMed]

Genemap99

We used data found in Genemap99 for gene and protein annotations in SOURCE.

Reference:


A Physical Map of 30,000 Human Genes
P. Deloukas, * G. D. Schuler, G. Gyapay, E. M. Beasley, C. Soderlund, P. Rodriguez-Tomé, L. Hui, T. C. Matise, K. B. McKusick, J. S. Beckmann, S. Bentolila, M.-T. Bihoreau, B. B. Birren, J. Browne, A. Butler, A. B. Castle, N. Chiannilkulchai, C. Clee, P. J. R. Day, A. Dehejia, T. Dibling, N. Drouot, S. Duprat, C. Fizames, S. Fox, S. Gelling, L. Green, P. Harrison, R. Hocking, E. Holloway, S. Hunt, S. Keil, P. Lijnzaad, C. Louis-Dit-Sully, J. Ma, A. Mendis, J. Miller, J. Morissette, D. Muselet, H. C. Nusbaum, A. Peck, S. Rozen, D. Simon, D. K. Slonim, R. Staples, L. D. Stein, E. A. Stewart, M. A. Suchard, T. Thangarajah, N. Vega-Czarny, C. Webber, X. Wu, J. Hudson, C. Auffray, N. Nomura, J. M. Sikela, M. H. Polymeropoulos, M. R. James, E. S. Lander, T. J. Hudson, R. M. Myers, D. R. Cox, J. Weissenbach, M. S. Boguski, D. R. Bentley:
Science 1998 Oct 23;282(5389):744-6 [PDF] [PubMed]

SwissProt

We used data found in SwissProt for gene and protein annotations in SOURCE.

Reference:


Bairoch A., Apweiler R.
The SWISS-PROT protein sequence database and its supplement
TrEMBL in 2000 Nucleic Acids Res. 28:45-48(2000). [PDF] [PubMed]

dbEST

We used data found in dbEST for gene and protein annotations in SOURCE.

Reference:


Nat Genet 1993 Aug;4(4):332-3
dbEST--database for "expressed sequence tags".
Boguski MS, Lowe TM, Tolstoshev CM. [PubMed]

UniGene

We used data found in UniGene for gene and protein annotations in SOURCE.

Reference:


An article about the UniGene Collection in the August 1997 NCBI News contains an overview of the project.


Schuler (1997)
Pieces of the puzzle: expressed sequence tags and the catalog of human genes.
J Mol Med 75(10),694-698. [PubMed] [PDF]


Boguski & Schuler (1995).
ESTablishing a human transcript map.
Nature Genetics 10, 369-371. [PubMed]

Caenorhabditis elegans

For C. elegans gene and protein annotations we used data found at:

WormPD/Proteome

Reference:


Costanzo, M.C., Crawford, M.E., Hirschman, J.E., Kranz, J.E., Olsen, P., Robertson, L.S., Skrzypek, M.S., Braun, B.R., Hopkins, K.L., Kondu, P., Lengieza, C., Lew-Smith, J.E., Tillberg, M., Garrels, J.I. (2001)
YPD^tm, PombePD^tm, and WormPD^tm: model organism volumes of the Bioknowledge^tm library, an integrated resource for protein information.
Nucleic Acids Research 29(1): 75-9. [PubMed] [PDF]


Costanzo, M.C., Hogan, J.D., Cusick, M.E., Davis, B.P., Fancher, A.M., Hodges, P.E., Kondu, P., Lengieza, C., Lew-Smith, J.E., Lingner, C., Roberg-Perez, K.J., Tillberg, M., Brooks, J.E., Garrels, J.I. (2000)
The Yeast Proteome Database (YPD) and Caenorhabditis elegans Proteome Database (WormPD): comprehensive resources for the organization and comparison of model organism protein information.
Nucleic Acids Research 28(1): 73-76. [PubMed] [PDF]

Campylobacter jejuni

For C. jejuni gene and protein annotations we used data found at:

Sanger Institute

Reference:


J. Parkhill, B.W. Wren, K. Mungall, J.M. Ketley, C. Churcher, D. Basham, T. Chillingworth, R.M. Davies, T. Feltwell, S. Holroyd, K. Jagels, A.V. Karlyshev, S. Moule, M.J. Pallen, C. W. Penn, M.A. Quail, M-A. Rajandream, K.M. Rutherford, A.H.M. van Vliet, S. Whitehead, and B.G. Barrell.
The genome sequence of the foodborne pathogen Campylobacter jejuni reveals hypervariable sequences.
Nature 403, 665-668 (2000). [PubMed] [PDF]

Escherichia coli

For E. coli gene and protein annotations we used data found at:

dbget/GenomeNet

Reference:


Kanehisa, M.: Linking databases and organisms: GenomeNet resources in Japan.
Trends Biochem Sci. 22, 442-444 (1997). [PubMed] [PDF]



Fujibuchi, W., Goto, S., Migimatsu, H., Uchiyama, I., Ogiwara, A., Akiyama, Y., and Kanehisa, M.:
DBGET/LinkDB: an integrated database retrieval system.
Pacific Symp. Biocomputing 1998, 683-694 (1997). [PubMed]

EcoCyc/MetaCyc

Reference:

Karp, P.D., Riley, M., Saier, M., Paulsen, I.T., Paley, S. and Pellegrini-Toole, A.
EcoCyc: Electronic Encyclopedia of E. coli Genes and Metabolism,
Nucleic Acids Research, 28(1):56 2000. [PubMed] [PDF]

Entamoeba histolytica

For E. histolytica gene and protein annotations we used data found at:

NCBI GenBank

Reference:


Wheeler DL, Chappey C, Lash AE, Leipe DD, Madden TL, Schuler GD, Tatusova TA, Rapp BA.
Database resources of the National Center for Biotechnology Information.
Nucleic Acids Res. 2000 Jan 1;28(1):10-4. [PubMed] [PDF]

Helicobacter pylori

For H. pylori gene and protein annotations we used data found at:

TIGR

Reference:


Tomb JF, White O, Kerlavage AR, Clayton RA, Sutton GG, Fleischmann RD, Ketchum KA, Klenk HP, Gill S, Dougherty BA, Nelson K, Quackenbush J, Zhou L, Kirkness EF, Peterson S, Loftus B, Richardson D, Dodson R, Khalak HG, Glodek A, McKenney K, Fitzegerald LM, Lee N, Adams MD, Venter JC, et al.
The complete genome sequence of the gastric pathogen Helicobacter pylori.
Nature. 1997 Aug 7;388(6642):539-47. [PubMed] [PDF]

AstraZeneca

Reference:


Alm RA, Ling LS, Moir DT, King BL, Brown ED, Doig PC, Smith DR, Noonan B, Guild BC, deJonge BL, Carmel G, Tummino PJ, Caruso A, Uria-Nickelsen M, Mills DM, Ives C, Gibson R, Merberg D, Mills SD, Jiang Q, Taylor DE, Vovis GF, Trust TJ.
Genomic-sequence comparison of two unrelated isolates of the human gastric pathogen Helicobacter pylori.
Nature. 1999 Jan 14;397(6715):176-80. [PubMed] [PDF]

Streptomyces coelicolor

For S. coelicolor gene and protein annotations we used data found at:

Sanger Institute

Reference:


(Not completed)

EMBL

Reference:


Stoesser G., Baker W., van den Broek A., Camon E., Garcia-Pastor M., Kanz C., Kulikova T., Lombard V., Lopez R., Parkinson H., Redaschi N., Sterk P., Stoehr P., Tuli MA.:
The EMBL Nucleotide Sequence Database.
Nucleic Acids Res 2001, Vol. 29 (1), 17-21 [PubMed] [PDF]

Mycobacterium tuberculosis

For M. tuberculosis gene and protein annotations we used data found at:

Sanger Insitute

Reference:


Cole S.T., Brosch R., Parkhill J., Garnier T., Churcher C., Harris D., Gordon S.V., Eiglmeier K., Gas S., Barry C.E.III., Tekaia F., Badcock K., Basham D., Brown D., Chillingworth T., Connor R., Davies R., Devlin K., Feltwell T., Gentles S., Hamlin N., Holroyd S., Hornsby T., Jagels K., Krogh A., McLean J., Moule S., Murphy L., Oliver K., Osborne J., Quail M.A., Rajandream, M-A., Rogers J., Rutter S., Seeger K., Skelton J., Squares S., Squares R., Sulston J.E., Taylor K., Whitehead S. and Barrell, B.G.
Deciphering the biology of Mycobacterium tuberculosis from the complete genome sequence.
Nature 393, 537-544 (1998). [PubMed] [PDF]

Institut Pasteur TubercuList

Reference:


Cole S.T., Brosch R., Parkhill J., Garnier T., Churcher C., Harris D., Gordon S.V., Eiglmeier K., Gas S., Barry C.E.III., Tekaia F., Badcock K., Basham D., Brown D., Chillingworth T., Connor R., Davies R., Devlin K., Feltwell T., Gentles S., Hamlin N., Holroyd S., Hornsby T., Jagels K., Krogh A., McLean J., Moule S., Murphy L., Oliver K., Osborne J., Quail M.A., Rajandream, M-A., Rogers J., Rutter S., Seeger K., Skelton J., Squares S., Squares R., Sulston J.E., Taylor K., Whitehead S. and Barrell, B.G.
Deciphering the biology of Mycobacterium tuberculosis from the complete genome sequence.
Nature 393, 537-544 (1998). [PubMed] [PDF]

Vibrio cholerae

For V. cholerae gene and protein annotations we used data found at:

TIGR

Reference:


Heidelberg JF, Eisen JA, Nelson WC, Clayton RA, Gwinn ML, Dodson RJ, Haft DH, Hickey EK, Peterson JD, Umayam L, Gill SR, Nelson KE, Read TD, Tettelin H, Richardson D, Ermolaeva MD, Vamathevan J, Bass S, Qin H, Dragoi I, Sellers P, McDonald L, Utterback T, Fleishmann RD, Nierman WC, White O.
DNA sequence of both chromosomes of the cholera pathogen Vibrio cholerae.
Nature. 2000 Aug 3;406(6795):477-83. [PubMed] [PDF]

Saccharomyces cerevisiae

For S. cerevisiae gene and protein annotations we used data found at:

SGD

Reference:


Cherry JM, Ball C, Weng S, Juvik G, Schmidt R, Adler C, Dunn B, Dwight S, Riles L, Mortimer RK, Botstein D
Genetic and physical maps of Saccharomyces cerevisiae.
Nature. 1997 May 29;387(6632 Suppl):67-73. [PubMed] [PDF]


Ball CA, Dolinski K, Dwight SS, Harris MA, Issel-Tarver L, Kasarskis A, Scafe CR, Sherlock G, Binkley G, Jin H, Kaloper M, Orr SD, Schroeder M, Weng S, Zhu Y, Botstein D, Cherry JM.
Integrating functional genomic information into the Saccharomyces genome database.
Nucleic Acids Res. 2000 Jan 1;28(1):77-80. [PubMed] [PDF]

Toxoplasma gondii

For T. gondii gene and protein annotations we used data found at:

ParaDB

Reference:


Ajioka, J.W., Boothroyd, J.C., Brunk, B.P., Hehl, A., Hillier, L., Manger, I.D., Marra, M., Overton, G.C., Roos, D.S., Wan, K.L., Waterston, R., Sibley, L.D. (1998)
Gene discovery by EST sequencing in Toxoplasma gondii reveals sequences restricted to the Apicomplexa.
Genome Res. 1998 Jan;8(1):18-28. [PubMed] [PDF]

Arabidopsis thaliana

For A. thaliana gene and protein annotations we used data found at:

TIGR

Reference:


Sequence and analysis of the Arabidopsis genome.
Bevan, M., Mayer, K., White, O., Eisen, J.A., Preuss, D., Bureau, T., Salzberg, S.L., Mewes, H.
Current Opinion Plant Biology Apr 1;4(2):105-110 (2001) [PubMed] [PDF]

The Arabidopsis Information Resource (TAIR)

Reference:



Huala, E; Dickerman, A; Garcia-Hernandez, M; Weems, D; Reiser, L; LaFond, F; Hanley, D; Kiphart, D; Zhuang, J; Huang, W; Mueller, L; Bhattacharyya, D; Bhaya, D; Sobral, B; Beavis, B, Somerville, C; and Rhee, SY
The Arabidopsis Information Resource (TAIR): A comprehensive database and web-based information retrieval, analysis, and visualization system for a model plant.
Nucleic Acids Res. 2001 Jan 1;29(1):102-5. [PubMed] [PDF]

NCBI

Reference:



Wheeler DL, Chappey C, Lash AE, Leipe DD, Madden TL, Schuler GD, Tatusova TA, Rapp BA.
Database resources of the National Center for Biotechnology Information.
Nucleic Acids Res. 2000 Jan 1;28(1):10-4. [PubMed] [PDF]