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EBIEMBL-EBI Web Servicesaboutwebservices

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about:webservices [2013/01/28 08:52]
hpm (172.22.68.212) 		about:webservices [2013/08/05 10:18] (current)
hpm (172.22.68.212)
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| [[http://www.ebi.ac.uk/ena/about/page.php?page=browser|ENA Browser]] | | Retrieval of sequence and associated records from [[http://www.ebi.ac.uk/ena/|ENA]] | | [[http://www.ebi.ac.uk/ena/about/page.php?page=browser|ENA Browser]] | | Retrieval of sequence and associated records from [[http://www.ebi.ac.uk/ena/|ENA]] |
| [[http://www.ebi.ac.uk/gxa/help/AtlasApis|Gene Expression Atlas API]] |  | Enriched database of summary statistics over a curated subset of ArrayExpress Archive | | [[http://www.ebi.ac.uk/gxa/help/AtlasApis|Gene Expression Atlas API]] |  | Enriched database of summary statistics over a curated subset of ArrayExpress Archive |
-| [[http://www.ebi.ac.uk/integr8/HelpAction.do?action=searchById&refId=59|Integr8 Web Service]] | | A subset of the data available from the [[http://www.ebi.ac.uk/integr8/|Integr8]] Web Portal. | 
| [[http://www.biomart.org/martservice.html|MartService]] | | Database search and data retrieval using [[http://www.biomart.org/|BioMart]]. | | [[http://www.biomart.org/martservice.html|MartService]] | | Database search and data retrieval using [[http://www.biomart.org/|BioMart]]. |
| [[http://code.google.com/p/psicquic/|PSICQUIC]] |  | Standardised access to molecular interaction databases, including [[http://www.ebi.ac.uk/chembl/|ChEMBL]], [[http://www.reactome.org/|Reactome]] and [[http://www.ebi.ac.uk/intact/|IntAct]]. | | [[http://code.google.com/p/psicquic/|PSICQUIC]] |  | Standardised access to molecular interaction databases, including [[http://www.ebi.ac.uk/chembl/|ChEMBL]], [[http://www.reactome.org/|Reactome]] and [[http://www.ebi.ac.uk/intact/|IntAct]]. |
| [[http://www.ebi.ac.uk/rhea/rest/1.0/|Rhea]] |  | Manually annotated database of chemical reactions | | [[http://www.ebi.ac.uk/rhea/rest/1.0/|Rhea]] |  | Manually annotated database of chemical reactions |
-| [[http://www.ebi.ac.uk/~srs/wiki/doku.php?id=guides:srsurlapi|SRS]] | | Database search and data retrieval using [[http://srs.ebi.ac.uk/|SRS@EBI]]. |+| [[http://www.ebi.ac.uk/~srs/wiki/doku.php?id=guides:srsurlapi|SRS]] | | Database search and data retrieval using [[http://srs.ebi.ac.uk/|SRS@EMBL-EBI]]. |
| [[http://www.uniprot.org/faq/28|UniProt.org]] | | The Universal Protein Resource (UniProt) a comprehensive resource for protein sequence and annotation data. | | [[http://www.uniprot.org/faq/28|UniProt.org]] | | The Universal Protein Resource (UniProt) a comprehensive resource for protein sequence and annotation data. |
| [[services:dbfetch_rest|WSDbfetch (REST)]] | [[services:dbfetch_rest#clients|WSDbfetch (REST)]] | Identifier based entry retrieval for various up-to-date biological databases. | | [[services:dbfetch_rest|WSDbfetch (REST)]] | [[services:dbfetch_rest#clients|WSDbfetch (REST)]] | Identifier based entry retrieval for various up-to-date biological databases. |
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==== Analysis Tools ==== ==== Analysis Tools ====
- 
-^ Service ^ Clients ^ Description ^ 
-| [[soaplab:overview|Soaplab]] | [[soaplab:guide|examples]] | Includes most EMBOSS applications that are suitable for launching through Web Services | 
^ REST Service ^ SOAP Service ^ Description ^ ^ REST Service ^ SOAP Service ^ Description ^
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^ REST Service ^ SOAP Service ^ Description ^ ^ REST Service ^ SOAP Service ^ Description ^
-| [[:services:pfa:iprscan_rest|InterProScan (REST)]] | [[:services:pfa:iprscan_soap|InterProScan (SOAP)]] | A tool that combines different protein signature recognition methods. | +| [[:services:pfa:FingerPRINTScan (REST)]] | [[:services:pfa:FingerPRINTScan(SOAP)]] | Identifying the closest matching PRINTS sequence motif fingerprints in a protein sequence. | 
-| [[:services:pfa:Phobius (REST)]] | [[:services:pfa:Phobius (SOAP)]] | Prediction of transmembrane topology and signal peptides from the amino acid sequence of a protein |+| [[:services:pfa:iprscan_rest|InterProScan 4.x (REST)]] | [[:services:pfa:iprscan_soap|InterProScan 4.x (SOAP)]] | A tool that combines different protein signature recognition methods. | 
 +| [[:services:pfa:HMMER hmmscan (REST)]] | [[:services:pfa:HMMER hmmscan (SOAP)]] | Search a database of Hidden Markov Models (HMMs) with a sequence to infer membership of a sequence family. | 
 +| [[:services:pfa:Phobius (REST)]] | [[:services:pfa:Phobius (SOAP)]] | Prediction of transmembrane topology and signal peptides from the amino acid sequence of a protein. | 
 +| [[:services:pfa:Pratt (REST)]] | [[:services:pfa:Pratt (SOAP)]] | Search for patterns conserved in sets of unaligned protein sequences. | 
 +| [[:services:pfa:ps_scan_rest|PROSITE Scan (REST)]] | [[:services:pfa:ps_scan_soap|PROSITE Scan (SOAP)]] | Comparing a protein sequence against the signatures in PROSITE (both patterns and profiles). |
| [[:services:pfa:RADAR (REST)]] | [[:services:pfa:RADAR (SOAP)]] | Detection and alignment of repeats in protein sequences. | | [[:services:pfa:RADAR (REST)]] | [[:services:pfa:RADAR (SOAP)]] | Detection and alignment of repeats in protein sequences. |
==== Sequence Similarity Search (SSS) ==== ==== Sequence Similarity Search (SSS) ====
 +
 +Identify potentially homologous sequences based on sequence similarity.
^ REST Service ^ SOAP Service ^ Description ^ ^ REST Service ^ SOAP Service ^ Description ^
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==== Multiple Sequence Alignment (MSA) ==== ==== Multiple Sequence Alignment (MSA) ====
 +
 +Alignment of a set of three or more, protein or nucleotide sequences.
^ REST Service ^ SOAP Service ^ Description ^ ^ REST Service ^ SOAP Service ^ Description ^
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==== Pairwise Sequence Alignment (PSA) ==== ==== Pairwise Sequence Alignment (PSA) ====
 +
 +Alignment of two sequences.
^ REST Service ^ SOAP Service ^ Description ^ ^ REST Service ^ SOAP Service ^ Description ^
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==== Sequence Format Conversion ==== ==== Sequence Format Conversion ====
 +
 +Convert between common sequence formats, or verify the formatting of a sequence.
^ REST Service ^ SOAP Service ^ Description ^ ^ REST Service ^ SOAP Service ^ Description ^
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==== Sequence Statistics ==== ==== Sequence Statistics ====
 +
 +Analyse a sequence to determine its properties and use statistics to assign significance.
^ REST Service ^ SOAP Service ^ Description ^ ^ REST Service ^ SOAP Service ^ Description ^
 +| [[:services:seqstats:EMBOSS cpgplot (REST)]]  | [[:services:seqstats:EMBOSS cpgplot (SOAP)]]  | EMBOSS cpgplot identifies and plots CpG islands in nucleotide sequence. |
 +| [[:services:seqstats:EMBOSS isochore (REST)]]  | [[:services:seqstats:EMBOSS isochore (SOAP)]]  | EMBOSS isochore plots isochores in DNA sequences. |
| [[:services:seqstats:EMBOSS pepinfo (REST)]]  | [[:services:seqstats:EMBOSS pepinfo (SOAP)]]  | EMBOSS pepinfo plots amino acid properties. | | [[:services:seqstats:EMBOSS pepinfo (REST)]]  | [[:services:seqstats:EMBOSS pepinfo (SOAP)]]  | EMBOSS pepinfo plots amino acid properties. |
| [[:services:seqstats:EMBOSS pepstats (REST)]]  | [[:services:seqstats:EMBOSS pepstats (SOAP)]]  | EMBOSS pepstats calculates protein properties such as molecular weight. | | [[:services:seqstats:EMBOSS pepstats (REST)]]  | [[:services:seqstats:EMBOSS pepstats (SOAP)]]  | EMBOSS pepstats calculates protein properties such as molecular weight. |
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==== Sequence Translation ==== ==== Sequence Translation ====
 +
 +Translate a coding nucleotide sequence in to a protein sequence, or back-translate from a protein sequence to a possible coding nucleotide sequence.
^ REST Service ^ SOAP Service ^ Description ^ ^ REST Service ^ SOAP Service ^ Description ^
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==== Structural Analysis ==== ==== Structural Analysis ====
 +
 +Analysis of macromolecular structures.
^ REST Service ^ SOAP Service ^ Description ^ ^ REST Service ^ SOAP Service ^ Description ^
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==== Literature and Ontologies ==== ==== Literature and Ontologies ====
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 +Look-up ontology terms and navigate ontology relationships or access and analyse the literature.
^ Service ^ Clients ^ Description ^ ^ Service ^ Clients ^ Description ^
| [[http://www.ebi.ac.uk/biomodels/webservices.html|BioModels]] | [[http://www.ebi.ac.uk/biomodels/webservices.html|BioModels]] | Storing, searching and retrieving published mathematical models of biological interest | | [[http://www.ebi.ac.uk/biomodels/webservices.html|BioModels]] | [[http://www.ebi.ac.uk/biomodels/webservices.html|BioModels]] | Storing, searching and retrieving published mathematical models of biological interest |
-| [[http://www.ebi.ac.uk/Tools/picr/|PICR]] | [[clients:picr|PICR]] | Protein Identifier Cross-Reference Service |+| [[http://www.ebi.ac.uk/Tools/picr/|PICR]] | | Protein Identifier Cross-Reference Service |
| [[http://www.ebi.ac.uk/QuickGO/WebServices.html|QuickGO]] | [[http://www.ebi.ac.uk/QuickGO/WebServices.html|QuickGO]] | Gene Ontology (GO) and Gene Ontology Annotation (GOA) databases | | [[http://www.ebi.ac.uk/QuickGO/WebServices.html|QuickGO]] | [[http://www.ebi.ac.uk/QuickGO/WebServices.html|QuickGO]] | Gene Ontology (GO) and Gene Ontology Annotation (GOA) databases |
| [[http://europepmc.org/WebServices|Europe PMC Web Service]] |  | Search [[http://europepmc.org/|Europe PubMed Central]] | | [[http://europepmc.org/WebServices|Europe PMC Web Service]] |  | Search [[http://europepmc.org/|Europe PubMed Central]] |
 
about/webservices.1359363166.txt · Last modified: 2013/01/28 08:52 by hpm
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