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Article: EuPathDB: a portal to eukaryotic pathogen databases

Aurrecoechea, Cristina / Brestelli, John / Brunk, Brian P / Fischer, Steve / Gajria, Bindu / Gao, Xin / Gingle, Alan / Grant, Greg / Harb, Omar S / Heiges, Mark / Innamorato, Frank / Iodice, John / Kissinger, Jessica C / Kraemer, Eileen T / Li, Wei / Miller, John A / Nayak, Vishal / Pennington, Cary / Pinney, Deborah F /

Roos, David S / Ross, Chris / Srinivasamoorthy, Ganesh / Stoeckert, Christian J. Jr / Thibodeau, Ryan / Treatman, Charles / Wang, Haiming

Nucleic acids research. 2010 Jan., v. 38, no. suppl_1

2010

Abstract: EuPathDB (http://EuPathDB.org; formerly ApiDB) is an integrated database covering the eukaryotic pathogens of the genera Cryptosporidium, Giardia, Leishmania, Neospora, Plasmodium, Toxoplasma, Trichomonas and TRYPANOSOMA: While each of these groups is ... ...

Abstract	EuPathDB (http://EuPathDB.org; formerly ApiDB) is an integrated database covering the eukaryotic pathogens of the genera Cryptosporidium, Giardia, Leishmania, Neospora, Plasmodium, Toxoplasma, Trichomonas and TRYPANOSOMA: While each of these groups is supported by a taxon-specific database built upon the same infrastructure, the EuPathDB portal offers an entry point to all these resources, and the opportunity to leverage orthology for searches across genera. The most recent release of EuPathDB includes updates and changes affecting data content, infrastructure and the user interface, improving data access and enhancing the user experience. EuPathDB currently supports more than 80 searches and the recently-implemented 'search strategy' system enables users to construct complex multi-step searches via a graphical interface. Search results are dynamically displayed as the strategy is constructed or modified, and can be downloaded, saved, revised, or shared with other database users.
Keywords	Cryptosporidium ; Giardia ; Leishmania ; Neospora ; Plasmodium ; Toxoplasma ; Trichomonas ; Trypanosoma ; databases ; infrastructure ; nucleic acids ; pathogens ; user interface
Language	English
Dates of publication	2010-01
Size	p. D415-D419.
Document type	Article
ZDB-ID	186809-3
ISSN	0301-5610 ; 0305-1048
ISSN	0301-5610 ; 0305-1048
Database	NAL-Catalogue (AGRICOLA)

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Article: PlasmoDB: a functional genomic database for malaria parasites

Aurrecoechea, Cristina / Brestelli, John / Brunk, Brian P / Dommer, Jennifer / Fischer, Steve / Gajria, Bindu / Gao, Xin / Gingle, Alan / Grant, Greg / Harb, Omar S / Heiges, Mark / Innamorato, Frank / Iodice, John / Kissinger, Jessica C / Kraemer, Eileen / Li, Wei / Miller, John A / Nayak, Vishal / Pennington, Cary /

Pinney, Deborah F / Roos, David S / Ross, Chris / Stoeckert, Christian J. Jr / Treatman, Charles / Wang, Haiming

Nucleic acids research. 2009 Jan., v. 37, no. suppl_1

2009

Abstract: PlasmoDB (http://PlasmoDB.org) is a functional genomic database for Plasmodium spp. that provides a resource for data analysis and visualization in a gene-by-gene or genome-wide scale. PlasmoDB belongs to a family of genomic resources that are housed ... ...

Abstract	PlasmoDB (http://PlasmoDB.org) is a functional genomic database for Plasmodium spp. that provides a resource for data analysis and visualization in a gene-by-gene or genome-wide scale. PlasmoDB belongs to a family of genomic resources that are housed under the EuPathDB (http://EuPathDB.org) Bioinformatics Resource Center (BRC) umbrella. The latest release, PlasmoDB 5.5, contains numerous new data types from several broad categories--annotated genomes, evidence of transcription, proteomics evidence, protein function evidence, population biology and evolution. Data in PlasmoDB can be queried by selecting the data of interest from a query grid or drop down menus. Various results can then be combined with each other on the query history page. Search results can be downloaded with associated functional data and registered users can store their query history for future retrieval or analysis.
Keywords	Plasmodium ; bioinformatics ; evolution ; genome ; malaria ; menu planning ; nucleic acids ; parasites ; proteomics ; transcription (genetics)
Language	English
Dates of publication	2009-01
Size	p. D539-D543.
Document type	Article
ZDB-ID	186809-3
ISSN	0301-5610 ; 0305-1048
ISSN	0301-5610 ; 0305-1048
Database	NAL-Catalogue (AGRICOLA)

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Article ; Online: PlasmoDB: a functional genomic database for malaria parasites.

Pinney, Deborah F / Roos, David S / Ross, Chris / Stoeckert, Christian J / Treatman, Charles / Wang, Haiming

Nucleic acids research

2009 Volume 37, Issue Database issue, Page(s) D539–43

Abstract	PlasmoDB (http://PlasmoDB.org) is a functional genomic database for Plasmodium spp. that provides a resource for data analysis and visualization in a gene-by-gene or genome-wide scale. PlasmoDB belongs to a family of genomic resources that are housed under the EuPathDB (http://EuPathDB.org) Bioinformatics Resource Center (BRC) umbrella. The latest release, PlasmoDB 5.5, contains numerous new data types from several broad categories--annotated genomes, evidence of transcription, proteomics evidence, protein function evidence, population biology and evolution. Data in PlasmoDB can be queried by selecting the data of interest from a query grid or drop down menus. Various results can then be combined with each other on the query history page. Search results can be downloaded with associated functional data and registered users can store their query history for future retrieval or analysis.
MeSH term(s)	Animals ; Databases, Genetic ; Genome, Protozoan ; Genomics ; Plasmodium/genetics ; Plasmodium/growth & development ; Plasmodium/metabolism ; Protozoan Proteins/genetics ; Protozoan Proteins/physiology ; Transcription, Genetic
Chemical Substances	Protozoan Proteins
Language	English
Publishing date	2009-01
Publishing country	England
Document type	Journal Article ; Research Support, N.I.H., Extramural
ZDB-ID	2205588-5
ISSN	1362-4962 ; 1746-8272 ; 0305-1048 ; 0261-3166
ISSN (online)	1362-4962 ; 1746-8272
ISSN	0305-1048 ; 0261-3166
DOI	10.1093/nar/gkn814
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article ; Online: EuPathDB: a portal to eukaryotic pathogen databases.

Roos, David S / Ross, Chris / Srinivasamoorthy, Ganesh / Stoeckert, Christian J / Thibodeau, Ryan / Treatman, Charles / Wang, Haiming

Nucleic acids research

2009 Volume 38, Issue Database issue, Page(s) D415–9

Abstract	EuPathDB (http://EuPathDB.org; formerly ApiDB) is an integrated database covering the eukaryotic pathogens of the genera Cryptosporidium, Giardia, Leishmania, Neospora, Plasmodium, Toxoplasma, Trichomonas and Trypanosoma. While each of these groups is supported by a taxon-specific database built upon the same infrastructure, the EuPathDB portal offers an entry point to all these resources, and the opportunity to leverage orthology for searches across genera. The most recent release of EuPathDB includes updates and changes affecting data content, infrastructure and the user interface, improving data access and enhancing the user experience. EuPathDB currently supports more than 80 searches and the recently-implemented 'search strategy' system enables users to construct complex multi-step searches via a graphical interface. Search results are dynamically displayed as the strategy is constructed or modified, and can be downloaded, saved, revised, or shared with other database users.
MeSH term(s)	Animals ; Computational Biology/methods ; Computational Biology/trends ; Databases, Genetic ; Databases, Nucleic Acid ; Databases, Protein ; Genome, Protozoan ; Humans ; Information Storage and Retrieval/methods ; Internet ; Protein Structure, Tertiary ; Protozoan Infections/genetics ; Protozoan Infections/parasitology ; Protozoan Proteins/genetics ; Software
Chemical Substances	Protozoan Proteins
Language	English
Publishing date	2009-11-13
Publishing country	England
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't ; Research Support, U.S. Gov't, P.H.S.
ZDB-ID	186809-3
ISSN	1362-4962 ; 1362-4954 ; 0301-5610 ; 0305-1048
ISSN (online)	1362-4962 ; 1362-4954
ISSN	0301-5610 ; 0305-1048
DOI	10.1093/nar/gkp941
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article: GiardiaDB and TrichDB: integrated genomic resources for the eukaryotic protist pathogens Giardia lamblia and Trichomonas vaginalis

Aurrecoechea, Cristina / Brestelli, John / Brunk, Brian P / Carlton, Jane M / Dommer, Jennifer / Fischer, Steve / Gajria, Bindu / Gao, Xin / Gingle, Alan / Grant, Greg / Harb, Omar S / Heiges, Mark / Innamorato, Frank / Iodice, John / Kissinger, Jessica C / Kraemer, Eileen / Li, Wei / Miller, John A / Morrison, Hilary G /

Nayak, Vishal / Pennington, Cary / Pinney, Deborah F / Roos, David S / Ross, Chris / Stoeckert, Christian J. Jr / Sullivan, Steven / Treatman, Charles / Wang, Haiming

Nucleic acids research. 2009 Jan., v. 37, no. suppl_1

2009

Abstract: GiardiaDB (http://GiardiaDB.org) and TrichDB (http://TrichDB.org) house the genome databases for Giardia lamblia and Trichomonas vaginalis, respectively, and represent the latest additions to the EuPathDB (http://EuPathDB.org) family of functional ... ...

Abstract	GiardiaDB (http://GiardiaDB.org) and TrichDB (http://TrichDB.org) house the genome databases for Giardia lamblia and Trichomonas vaginalis, respectively, and represent the latest additions to the EuPathDB (http://EuPathDB.org) family of functional genomic databases. GiardiaDB and TrichDB employ the same framework as other EuPathDB sites (CryptoDB, PlasmoDB and ToxoDB), supporting fully integrated and searchable databases. Genomic-scale data available via these resources may be queried based on BLAST searches, annotation keywords and gene ID searches, GO terms, sequence motifs and other protein characteristics. Functional queries may also be formulated, based on transcript and protein expression data from a variety of platforms. Phylogenetic relationships may also be interrogated. The ability to combine the results from independent queries, and to store queries and query results for future use facilitates complex, genome-wide mining of functional genomic data.
Keywords	Giardia lamblia ; Trichomonas vaginalis ; genes ; genetic databases ; genome mining ; nucleic acids ; pathogens ; phylogeny ; protein synthesis ; protists
Language	English
Dates of publication	2009-01
Size	p. D526-D530.
Document type	Article
ZDB-ID	186809-3
ISSN	0301-5610 ; 0305-1048
ISSN	0301-5610 ; 0305-1048
Database	NAL-Catalogue (AGRICOLA)

In stock of ZB MED Bonn / Germany

Z 79/704: Show issues

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Article: TriTrypDB: a functional genomic resource for the Trypanosomatidae

Aslett, Martin / Aurrecoechea, Cristina / Berriman, Matthew / Brestelli, John / Brunk, Brian P / Carrington, Mark / Depledge, Daniel P / Fischer, Steve / Gajria, Bindu / Gao, Xin / Gardner, Malcolm J / Gingle, Alan / Grant, Greg / Harb, Omar S / Heiges, Mark / Hertz-Fowler, Christiane / Houston, Robin / Innamorato, Frank / Iodice, John /

Kissinger, Jessica C / Kraemer, Eileen / Li, Wei / Logan, Flora J / Miller, John A / Mitra, Siddhartha / Myler, Peter J / Nayak, Vishal / Pennington, Cary / Phan, Isabelle / Pinney, Deborah F / Ramasamy, Gowthaman / Rogers, Matthew B / Roos, David S / Ross, Chris / Sivam, Dhileep / Smith, Deborah F / Srinivasamoorthy, Ganesh / Stoeckert, Christian J. Jr / Subramanian, Sandhya / Thibodeau, Ryan / Tivey, Adrian / Treatman, Charles / Velarde, Giles / Wang, Haiming

Nucleic acids research. 2010 Jan., v. 38, no. suppl_1

2010

Abstract: TriTrypDB (http://tritrypdb.org) is an integrated database providing access to genome-scale datasets for kinetoplastid parasites, and supporting a variety of complex queries driven by research and development needs. TriTrypDB is a collaborative project, ... ...

Abstract	TriTrypDB (http://tritrypdb.org) is an integrated database providing access to genome-scale datasets for kinetoplastid parasites, and supporting a variety of complex queries driven by research and development needs. TriTrypDB is a collaborative project, utilizing the GUS/WDK computational infrastructure developed by the Eukaryotic Pathogen Bioinformatics Resource Center (EuPathDB.org) to integrate genome annotation and analyses from GeneDB and elsewhere with a wide variety of functional genomics datasets made available by members of the global research community, often pre-publication. Currently, TriTrypDB integrates datasets from Leishmania braziliensis, L. infantum, L. major, L. tarentolae, Trypanosoma brucei and T. cruzi. Users may examine individual genes or chromosomal spans in their genomic context, including syntenic alignments with other kinetoplastid organisms. Data within TriTrypDB can be interrogated utilizing a sophisticated search strategy system that enables a user to construct complex queries combining multiple data types. All search strategies are stored, allowing future access and integrated searches. 'User Comments' may be added to any gene page, enhancing available annotation; such comments become immediately searchable via the text search, and are forwarded to curators for incorporation into the reference annotation when appropriate.
Keywords	Leishmania braziliensis ; Trypanosoma brucei ; bioinformatics ; data collection ; databases ; genes ; genomics ; infrastructure ; nucleic acids ; parasites ; pathogens ; research and development
Language	English
Dates of publication	2010-01
Size	p. D457-D462.
Document type	Article
ZDB-ID	186809-3
ISSN	0301-5610 ; 0305-1048
ISSN	0301-5610 ; 0305-1048
Database	NAL-Catalogue (AGRICOLA)

In stock of ZB MED Bonn / Germany

Z 79/704: Show issues

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Article ; Online: GiardiaDB and TrichDB: integrated genomic resources for the eukaryotic protist pathogens Giardia lamblia and Trichomonas vaginalis.

Nayak, Vishal / Pennington, Cary / Pinney, Deborah F / Roos, David S / Ross, Chris / Stoeckert, Christian J / Sullivan, Steven / Treatman, Charles / Wang, Haiming

Nucleic acids research

2008 Volume 37, Issue Database issue, Page(s) D526–30

Abstract	GiardiaDB (http://GiardiaDB.org) and TrichDB (http://TrichDB.org) house the genome databases for Giardia lamblia and Trichomonas vaginalis, respectively, and represent the latest additions to the EuPathDB (http://EuPathDB.org) family of functional genomic databases. GiardiaDB and TrichDB employ the same framework as other EuPathDB sites (CryptoDB, PlasmoDB and ToxoDB), supporting fully integrated and searchable databases. Genomic-scale data available via these resources may be queried based on BLAST searches, annotation keywords and gene ID searches, GO terms, sequence motifs and other protein characteristics. Functional queries may also be formulated, based on transcript and protein expression data from a variety of platforms. Phylogenetic relationships may also be interrogated. The ability to combine the results from independent queries, and to store queries and query results for future use facilitates complex, genome-wide mining of functional genomic data.
MeSH term(s)	Animals ; Databases, Genetic ; Genome, Protozoan ; Genomics ; Giardia lamblia/genetics ; Software ; Systems Integration ; Trichomonas vaginalis/genetics
Language	English
Publishing date	2008-09-29
Publishing country	England
Document type	Journal Article ; Research Support, N.I.H., Extramural
ZDB-ID	186809-3
ISSN	1362-4962 ; 1362-4954 ; 0301-5610 ; 0305-1048
ISSN (online)	1362-4962 ; 1362-4954
ISSN	0301-5610 ; 0305-1048
DOI	10.1093/nar/gkn631
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Zs.A 1067: Show issues

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Je nach Verfügbarkeit (siehe Angabe bei Bestand)
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Jg. 1995 - 2021: Lesesall (1.OG)
ab Jg. 2022: Lesesaal (EG)

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Article ; Online: TriTrypDB: a functional genomic resource for the Trypanosomatidae.

Kissinger, Jessica C / Kraemer, Eileen / Li, Wei / Logan, Flora J / Miller, John A / Mitra, Siddhartha / Myler, Peter J / Nayak, Vishal / Pennington, Cary / Phan, Isabelle / Pinney, Deborah F / Ramasamy, Gowthaman / Rogers, Matthew B / Roos, David S / Ross, Chris / Sivam, Dhileep / Smith, Deborah F / Srinivasamoorthy, Ganesh / Stoeckert, Christian J / Subramanian, Sandhya / Thibodeau, Ryan / Tivey, Adrian / Treatman, Charles / Velarde, Giles / Wang, Haiming

Nucleic acids research

2009 Volume 38, Issue Database issue, Page(s) D457–62

Abstract	TriTrypDB (http://tritrypdb.org) is an integrated database providing access to genome-scale datasets for kinetoplastid parasites, and supporting a variety of complex queries driven by research and development needs. TriTrypDB is a collaborative project, utilizing the GUS/WDK computational infrastructure developed by the Eukaryotic Pathogen Bioinformatics Resource Center (EuPathDB.org) to integrate genome annotation and analyses from GeneDB and elsewhere with a wide variety of functional genomics datasets made available by members of the global research community, often pre-publication. Currently, TriTrypDB integrates datasets from Leishmania braziliensis, L. infantum, L. major, L. tarentolae, Trypanosoma brucei and T. cruzi. Users may examine individual genes or chromosomal spans in their genomic context, including syntenic alignments with other kinetoplastid organisms. Data within TriTrypDB can be interrogated utilizing a sophisticated search strategy system that enables a user to construct complex queries combining multiple data types. All search strategies are stored, allowing future access and integrated searches. 'User Comments' may be added to any gene page, enhancing available annotation; such comments become immediately searchable via the text search, and are forwarded to curators for incorporation into the reference annotation when appropriate.
MeSH term(s)	Animals ; Computational Biology/methods ; Computational Biology/trends ; Databases, Genetic ; Databases, Nucleic Acid ; Databases, Protein ; Genome, Protozoan ; Information Storage and Retrieval/methods ; Internet ; Leishmania/genetics ; Protein Structure, Tertiary ; Protozoan Proteins/genetics ; Software ; Trypanosoma/genetics ; User-Computer Interface
Chemical Substances	Protozoan Proteins
Language	English
Publishing date	2009-10-20
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't ; Research Support, U.S. Gov't, P.H.S.
ZDB-ID	186809-3
ISSN	1362-4962 ; 1362-4954 ; 0301-5610 ; 0305-1048
ISSN (online)	1362-4962 ; 1362-4954
ISSN	0301-5610 ; 0305-1048
DOI	10.1093/nar/gkp851
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Zs.A 1067: Show issues

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ab Jg. 2022: Lesesaal (EG)

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Article: GiardiaDB and TrichDB : integrated genomic resources for the eukaryotic protist pathogens Giardia lamblia and Trichomonas vaginalis

Aurrecoechea, Cristina / Brestelli, John / Brunk, Brian P. / Carlton, Jane M. / Dommer, Jennifer / Fischer, Steve / Gajria, Bindu / Gao, Xin / Gingle, Alan / Grant, Greg / Harb, Omar S. / Heiges, Mark / Innamorato, Frank / Iodice, John / Kissinger, Jessica C. / Kraemer, Eileen / Li, Wei / Miller, John A. / Morrison, Hilary G. /

Nayak, Vishal / Pennington, Cary / Pinney, Deborah F. / Roos, David S. / Ross, Chris / Stoeckert, Christian J. / Sullivan, Steven / Treatman, Charles / Wang, Haiming

Abstract	GiardiaDB (http://GiardiaDB.org) and TrichDB (http://TrichDB.org) house the genome databases for Giardia lamblia and Trichomonas vaginalis, respectively, and represent the latest additions to the EuPathDB (http://EuPathDB.org) family of functional genomic databases. GiardiaDB and TrichDB employ the same framework as other EuPathDB sites (CryptoDB, PlasmoDB and ToxoDB), supporting fully integrated and searchable databases. Genomic-scale data available via these resources may be queried based on BLAST searches, annotation keywords and gene ID searches, GO terms, sequence motifs and other protein characteristics. Functional queries may also be formulated, based on transcript and protein expression data from a variety of platforms. Phylogenetic relationships may also be interrogated. The ability to combine the results from independent queries, and to store queries and query results for future use facilitates complex, genome-wide mining of functional genomic data.
Language	en_us
Document type	Article
Database	AGRIS - International Information System for the Agricultural Sciences and Technology

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