Franck Tanoh (2 months ago)
Allows access and the retrieval of information from the e-Fungi warehouse, an integrated data from multiple fungal genomes.
Franck Tanoh
Profile
Display Name:
Franck Tanoh
Email address:
ytanoh [at] cs.man.ac.uk
Affiliation:
University of Manchester
Country:
United Kingdom
Services Submitted (106)
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 82
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Annotations: 330
 321
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 5
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by Franck Tanoh (2 months ago)
Franck Tanoh (2 months ago) |
Provider:
e-Fungi
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Submitter / Source:
WSDL Location:
http://beaconw.cs.manchester.ac.uk/axis/services/efungi?wsdl |
92 SOAP Operations
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97
0
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Annotations: 27
7
20
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by Franck Tanoh (about 1 year ago)
Franck Tanoh (about 1 year ago)
Term management system.
Web Interface: http://www.nactem.ac.uk/software/termine/
by George Moulton (9 months ago)
George Moulton (9 months ago)
Input some source text and retrieve a list of terms discovered, ranked by their importance within the text.
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Provider:
Nactem
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Submitter / Source:
WSDL Location:
http://www.nactem.ac.uk/software/termine/webservice/termine.wsdl |
1 SOAP Operation
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81
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Annotations: 15
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15
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by Rodrigo Lopez (about 1 year ago)
Rodrigo Lopez (about 1 year ago)
EFetch: Retrieves records in the requested format from a list of one or more UIs or from user's environment.
Base URL: http://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?
by Pieter Neerincx (9 months ago)
Pieter Neerincx (9 months ago)
The EFetch services retrieve records in the requested format from several databases hosted by the NCBI.
by Pieter Neerincx (9 months ago)
Pieter Neerincx (9 months ago)
Note: this service is poorly documented on the NCBI site like in there is no documentation at all. I tried searching with NLM IDs in a similar way like for the well documented eFetchPubmed and eFetchPmc services, but could not make it work... Therefore there are no example inputs nor example outputs listed here.
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Provider:
National Center for Biotechnology Information (NCBI)
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Submitter / Source:
WSDL Location:
http://www.ncbi.nlm.nih.gov/entrez/eutils/soap/v2.0/efetch_nlmc.wsdl |
1 SOAP Operation
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195
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Annotations: 22
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22
0
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by Pieter Neerincx (9 months ago)
Pieter Neerincx (9 months ago)
The EFetch services retrieve records in the requested format from several databases hosted by the NCBI.
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Provider:
National Center for Biotechnology Information (NCBI)
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Submitter / Source:
WSDL Location:
http://www.ncbi.nlm.nih.gov/entrez/eutils/soap/v2.0/efetch_pubmed.wsdl |
1 SOAP Operation
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126
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Annotations: 27
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27
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by Rodrigo Lopez (about 1 year ago)
Rodrigo Lopez (about 1 year ago)
Entrez Programming Utilities are tools that provide access to Entrez data outside of the regular web query interface and may be helpful for retrieving search results for future use in another environment.
Home: http://www.ncbi.nlm.nih.gov/entrez/query/static/eutils_help.html
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Provider:
National Center for Biotechnology Information (NCBI)
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Submitter / Source:
WSDL Location:
http://www.ncbi.nlm.nih.gov/entrez/eutils/soap/eutils.wsdl |
14 SOAP Operations
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58
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Annotations: 35
6
7
22
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by Franck Tanoh (6 months ago)
Franck Tanoh (6 months ago)
A service for getting DDBJ ( http://www.biocatalogue.org/service_providers/4 ) service results which are called asynchronously.
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Provider:
DNA Data Bank of Japan (DDBJ)
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Submitter / Source:
WSDL Location:
http://xml.nig.ac.jp/wsdl/RequestManager.wsdl |
2 SOAP Operations
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71
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Annotations: 60
12
12
36
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by Franck Tanoh (6 months ago)
Franck Tanoh (6 months ago)
Retrieve tree information by GO ID. The Gene Ontology (GO) project provides a controlled vocabulary to describe gene and gene product attributes in any organism.
Website: http://www.geneontology.org/
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Provider:
DNA Data Bank of Japan (DDBJ)
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Submitter / Source:
WSDL Location:
http://xml.nig.ac.jp/wsdl/GO.wsdl |
3 SOAP Operations
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127
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Annotations: 80
14
19
47
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by Franck Tanoh (6 months ago)
Franck Tanoh (6 months ago)
Get OMIM (Online Mendelian Inheritance in Man) Information.
OMIM is a catalogue of a human genes and genetic disorders authored and edited by Dr. Victor A.McKusick and his colleagues at Johns Hopkins and elsewhere, and developed for the World Wide Web by NCBI, the National Center for Biotechnology Information.
Website: http://www.ncbi.nlm.nih.gov/sites/entrez?db=omim
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Provider:
DNA Data Bank of Japan (DDBJ)
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Submitter / Source:
WSDL Location:
http://xml.nig.ac.jp/wsdl/OMIM.wsdl |
4 SOAP Operations
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53
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Annotations: 126
30
6
90
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by Franck Tanoh (6 months ago)
Franck Tanoh (6 months ago)
NCBI Genome annotation is a summary of NCBI genome database focused on the gene annotation. This service provides users with gene annotation of human and mouse genome.
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Provider:
DNA Data Bank of Japan (DDBJ)
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Submitter / Source:
WSDL Location:
http://xml.nig.ac.jp/wsdl/NCBIGenomeAnnotation.wsdl |
7 SOAP Operations
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243
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Annotations: 145
30
17
98
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by Franck Tanoh (4 months ago)
Franck Tanoh (4 months ago)
This service allows you to access Ensembl.
Ensembl is a joint project between EMBL - EBI and the Sanger Institute to develop a software system which produces and maintains automatic annotation on selected eukaryotic genomes.
Ensembl website: http://www.ensembl.org/index.html
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Provider:
DNA Data Bank of Japan (DDBJ)
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Submitter / Source:
WSDL Location:
http://xml.nig.ac.jp/wsdl/Ensembl.wsdl |
7 SOAP Operations
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Other Services Responsible For (0)
No entries found
Services Annotated (333)
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50
0
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This service has been archived because it may not be active anymore (or is close to being non active).
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50
0
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Annotations: 8
3
3
2
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from
provider's description doc
(3 months ago)
provider's description doc
(3 months ago)
Authority: arabidopsis.info - Retrieves NASCArrays experiment description for a given slide name, Nottingham Arabidopsis Stock Centre's microarray database (http://affy.arabidopsis.info). Example input: 'Durrant_1-1_wild-type_Rep1_ATH1'.
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Provider:
University of Nottingham
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Submitter / Source:
WSDL Location:
http://biomoby.org/services/wsdl/arabidopsis.info/getNASCArraysExpDescriptionByNASCArraysSlide |
1 SOAP Operation
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62
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Annotations: 9
3
4
2
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from
provider's description doc
(3 months ago)
provider's description doc
(3 months ago)
Authority: arabidopsis.info - Retrieves NASCArrays experiment description for a given from NASCArrays reference number from NASCArrays, Nottingham Arabidopsis Stock Centre's microarray database (http://affy.arabidopsis.info). Example input: NASCARRAYS-136.
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Provider:
University of Nottingham
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Submitter / Source:
WSDL Location:
http://biomoby.org/services/wsdl/arabidopsis.info/getNASCArraysExpDescriptionByReferenceNumber |
1 SOAP Operation
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48
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Annotations: 7
3
2
2
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from
provider's description doc
(3 months ago)
provider's description doc
(3 months ago)
Authority: arabidopsis.info - Retrieves the NASCArrays reference number for a given NASC stock code from NASCArrays, Nottingham Arabidopsis Stock Centre's microarray database (http://affy.arabidopsis.info). Example input: 'NW20'.
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Provider:
University of Nottingham
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Submitter / Source:
WSDL Location:
http://biomoby.org/services/wsdl/arabidopsis.info/getNASCArraysReferenceNumberByNASCstockCode |
1 SOAP Operation
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51
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This service has been archived because it may not be active anymore (or is close to being non active).
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64
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This service has been archived because it may not be active anymore (or is close to being non active).
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57
0
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This service has been archived because it may not be active anymore (or is close to being non active).
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50
0
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Annotations: 8
3
2
3
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from
provider's description doc
(3 months ago)
provider's description doc
(3 months ago)
Authority: www.nias.affrc.go.jp - Get Reporters of microarray corresponding to a transcript.
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Provider:
National Institute of Agrobiological Sciences (NIAS)
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Submitter / Source:
WSDL Location:
http://biomoby.org/services/wsdl/www.nias.affrc.go.jp/getReportersOfTranscript |
1 SOAP Operation
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60
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Annotations: 8
3
2
3
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from
provider's description doc
(3 months ago)
provider's description doc
(3 months ago)
Authority: arabidopsis.info - Runs the NASCArrays analysis tool, GeneSwinger for a given AGI locus code. (http://affy.arabidopsis.info). This tool allows you to find interesting experiments for a gene. It shows you experiments where the gene you choose is highly variable, over all the experiments in the database. See the NASCArrays website for more details on what this does and how to use it (http://affymetrix.arabidopsis.info/internal/help/helpgeneswinger.html). Example input: At3g52590.
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Provider:
University of Nottingham
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Submitter / Source:
WSDL Location:
http://biomoby.org/services/wsdl/arabidopsis.info/NASCArraysGeneswingerByAGI |
1 SOAP Operation
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60
0
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This service has been archived because it may not be active anymore (or is close to being non active).
Favourites (8)
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795
 2
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aka
WSDbfetch (RPC/encoded SOAP)
aka
WSDbfetch (SOAP)
aka
WSDbfetch
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Annotations: 126
28
98
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by Franck Tanoh (9 months ago)
Franck Tanoh (9 months ago)
The service retrieves entries (sequences, literature abstract, protein structure information, etc) from various up-to-date biological databases using databases entry identifiers or accession numbers.
Supported databases (complete list can be found on the web interface): EMBL, Ensembl, UniProt, UniRef, UniSave, RefSeq, Medline, PDB, InterPro, HGVbase, GenomeReviews, interPro.
Web interface: http://www.ebi.ac.uk/cgi-bin/dbfetch
by Hamish McWilliam (3 months ago)
Hamish McWilliam (3 months ago)
An equivalent document/literal SOAP interface to the service is also available (http://www.biocatalogue.org/services/2654).
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Provider:
European Bioinformatics Institute (EBI)
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Submitter / Source:
WSDL Location:
http://www.ebi.ac.uk/Tools/webservices/wsdl/WSDbfetch.wsdl |
7 SOAP Operations
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301
1
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aka
WSInterProScan
aka
InterProScan
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Annotations: 72
29
41
2
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by joecker (9 months ago)
joecker (9 months ago)
InterProScan runs a lot of tools for protein domain prediction (against different databases). The results are mapped to InterPro identifiers to get additional information and identify same domains in different databases.
Please note that not all protein domains are included in InterPro, but are in the result of InterProScan.
by joecker (9 months ago)
joecker (9 months ago)
Please note that some tools in InterProScan use Hidden Markow Models and are therefore very slow.
by Franck Tanoh (9 months ago)
Franck Tanoh (9 months ago)
InterPro is a database of protein families, domains, regions, repeats and sites in which identifiable features found in known proteins can be applied to new protein sequences. This service allows you to query your protein sequence or protein sequence identifier against InterPro.
Home: http://www.ebi.ac.uk/Tools/InterProScan/
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Provider:
European Bioinformatics Institute (EBI)
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Submitter / Source:
WSDL Location:
http://www.ebi.ac.uk/Tools/webservices/wsdl/WSInterProScan.wsdl |
7 SOAP Operations
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319
1
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aka
EasyGene
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Annotations: 28
1
20
7
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from
provider's description doc
(about 1 year ago)
provider's description doc
(about 1 year ago)
The EasyGene 1.0 server produces a list of predicted genes given a sequence of prokaryotic
DNA. Each prediction is attributed with a significance score (R-value) indicating how likely
it is to be just a non-coding open reading frame rather than a real gene. The user needs
only to specify the organism hosting the query sequence. Two more parameters (start codon
leniency and R-value cutoff) have default values which may be altered if needed.
http://www.cbs.dtu.dk/services/EasyGene/
This service is fully asynchronous; the usage is split into the following
three operations, which is usually executed in this order.
Procedures and messages used are either common and shared ...
by Franck Tanoh (about 1 year ago)
Franck Tanoh (about 1 year ago)
Produces a list of predicted genes given a sequence of prokaryotic DNA.
Interface: http://www.cbs.dtu.dk/services/EasyGene/
by rapacki (6 months ago)
rapacki (6 months ago)
The EasyGene 1.0 server produces a list of predicted genes given a sequence of prokaryotic
DNA. Each prediction is attributed with a significance score (R-value) indicating how likely
it is to be just a non-coding open reading frame rather than a real gene. The user needs
only to specify the organism hosting the query sequence. Two more parameters (start codon
leniency and R-value cutoff) have default values which may be altered if needed.
Alongside this Web Service EasyGene method is also implemented as an interactive server at: http://www.cbs.dtu.dk/services/EasyGene/
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Provider:
Center for Biological Sequence Analysis (CBS)
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Submitter / Source:
WSDL Location:
http://www.cbs.dtu.dk/ws/EasyGene/EasyGene_1_2a_ws0.wsdl |
3 SOAP Operations
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547
2
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Annotations: 1283
192
15
1076
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by Franck Tanoh (about 1 year ago)
Franck Tanoh (about 1 year ago)
KEGG (Kyoto Encyclopedia of Genes and Genomes) is a database of biological systems, consisting of genetic building blocks of genes and proteins (KEGG GENES), chemical building blocks of both endogenous and exogenous substances (KEGG LIGAND), molecular wiring diagrams of interaction and reaction networks (KEGG PATHWAY), and hierarchies and relationships of various biological objects (KEGG BRITE). KEGG provides a reference knowledge base for linking genomes to biological systems and also to environments by the processes of PATHWAY mapping and BRITE mapping.
This service allows you to access or retrieve data (genes, pathways, enzyme, drugs, etc) from KEGG.
KEGG home page: http://www.g...
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Provider:
KEGG
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Submitter / Source:
WSDL Location:
http://soap.genome.jp/KEGG.wsdl |
72 SOAP Operations
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184
1
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aka
PICR
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Annotations: 28
9
19
0
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by Rodrigo Lopez (about 1 year ago)
Rodrigo Lopez (about 1 year ago)
Each major protein database uses its own conventions when assigning protein identifiers. Resolving the various, potentially unstable, identifiers that refer to identical proteins is a major challenge. This is a common problem when attempting to unify datasets that have been annotated with proteins from multiple data sources or querying data providers with one flavour of protein identifiers when the source database uses another.
The Protein Identifier Cross-Reference (PICR) service is a web application that provides interactive and programmatic (SOAP and REST) access to a mapping algorithm that uses the UniProt Archive (UniParc) as a data warehouse to offer protein cross-references base...
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Provider:
European Bioinformatics Institute (EBI)
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Submitter / Source:
WSDL Location:
http://www.ebi.ac.uk/Tools/picr/service?wsdl |
3 SOAP Operations
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121
1
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aka
http://code.google.com/p/psicquic/wiki/RestAccess
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Annotations: 6
0
6
0
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by brunoaranda (9 months ago)
brunoaranda (9 months ago)
PSICQUIC is an effort from the HUPO Proteomics Standard Initiative (HUPO-PSI) to standardise the access to molecular interaction databases programmatically.
This specific implementation provides remote access to the MINT database.
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Provider:
Protemics Standard Initiative Common Query InterfaCe (PSICQUIC)
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Submitter / Source:
Base URL:
http://mint.bio.uniroma2.it/mint/psicquic/webservices/current/search/version |
0 REST Endpoints
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128
1
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Annotations: 30
3
15
12
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by Franck Tanoh (about 1 year ago)
Franck Tanoh (about 1 year ago)
The TFmodeller program scans a protein sequence P against a library of protein-DNA complexes and builds comparative models of P if good templates are found. These models are used to get an idea of the P-DNA interface, its evolution and the putative recognised DNA sequences.
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Provider:
University of Mexico (Center for Genomic Sciences of the National Autonomous)
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Submitter / Source:
WSDL Location:
http://maya.ccg.unam.mx:8080/axis/TFmodellerService.jws?WSDL |
1 SOAP Operation
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154
1
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Annotations: 99
23
76
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by Franck Tanoh (about 1 year ago)
Franck Tanoh (about 1 year ago)
Retrieves information from the database of protein subcellular localization (DBSubLoc). This database contains proteins from primary protein database such as SWISS-PROT and PIR. By collecting the subcellular localization annotation, these information are classified and categorized by cross referencs to taxonomies and Gene Ontology database.
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Provider:
Institute of Bioinformatics, Tsinghua University
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Submitter / Source:
WSDL Location:
http://www.bioinfo.tsinghua.edu.cn/~tigerchen/SubLoc.wsdl |
7 SOAP Operations
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