spacer
spacer

Differences

This shows you the differences between two versions of the page.

about:webservices [2012/09/11 11:10]
hpm (172.22.68.212) Addition of new DaliLite and MaxSprout services and the sequence format conversion category.
about:webservices [2014/06/30 10:59] (current)
ympark (172.22.68.30)
Line 5: Line 5:
The [[http://www.ebi.ac.uk/|EMBL-EBI]] provides programmatic access to various data resources and analysis tools via. Web Services technologies. The [[http://www.ebi.ac.uk/|EMBL-EBI]] provides programmatic access to various data resources and analysis tools via. Web Services technologies.
-Web Services is an integration and inter-operation technology, to ensure client and server software from various sources will work well together, the technology is built on open standards:+Web Services is an integration and inter-operation technology. To ensure client and server software from various sources will work well together, the technology is built on open standards:
  * [[:tutorials:02_REST|Representational state transfer]] (REST): a software architecture style.   * [[:tutorials:02_REST|Representational state transfer]] (REST): a software architecture style.
  * [[:tutorials:03_SOAP|Simple Object Access Protocol]] (SOAP): a messaging protocol for transporting information.   * [[:tutorials:03_SOAP|Simple Object Access Protocol]] (SOAP): a messaging protocol for transporting information.
  * [[:tutorials:04_WSDL|Web Services Description Language]] (WSDL): a method for describing Web Services and their capabilities.   * [[:tutorials:04_WSDL|Web Services Description Language]] (WSDL): a method for describing Web Services and their capabilities.
-For the transport layer Web Services utilise common network protocols, generally the [[http://www.w3.org/Protocols/|Hypertext Transfer Protocol]] (HTTP).+For the transport layer Web Services utilise common network protocols, typically the [[http://www.w3.org/Protocols/|Hypertext Transfer Protocol]] (HTTP) used to provide access to web sites.
For an overview of Web Services technologies and short tutorials on using common programming languages and Web Services tool-kits see [[:tutorials:01_Intro|Introduction to Web Services]]. For an overview of Web Services technologies and short tutorials on using common programming languages and Web Services tool-kits see [[:tutorials:01_Intro|Introduction to Web Services]].
Line 16: Line 16:
===== Important Note ===== ===== Important Note =====
-**We kindly ask users to submit NO MORE THAN 25 JOBS AT THE TIME AND NOT TO SUBMIT MORE JOBS UNTIL YOU HAVE OBTAINED RESULTS FOR THE LAST 25. There are many people using these services and a fair share policy has been implemented that allows us to block users that submit jobs in a manner that prevents others from using the service. This block may affect access to the EMBL-EBI Web Services for an entire organisation or a class B or C subnet. Also make sure you USE A REAL EMAIL ADDRESS in your submissions. Using a fake email means we cannot contact you and will very likely result in your jobs being killed and your IP, Organisation or entire domain being black-listed. We do apologise for any inconvenience this may cause.**+**We kindly ask users to submit NO MORE THAN 30 JOBS AT THE TIME AND NOT TO SUBMIT MORE JOBS UNTIL YOU HAVE OBTAINED RESULTS FOR THE LAST 30. There are many people using these services and a fair share policy has been implemented that allows us to block users that submit jobs in a manner that prevents others from using the service. This block may affect access to the EMBL-EBI Web Services for an entire organisation or a class B or C subnet. Also make sure you USE A REAL EMAIL ADDRESS in your submissions. Using a fake email means we cannot contact you and will very likely result in your jobs being killed and your IP, Organisation or entire domain being black-listed. We do apologise for any inconvenience this may cause.**
===== Web Services ===== ===== Web Services =====
-A list of Web Services provided by EMBL-EBI follows. For services from other providers (e.g. [[http://www.ddbj.nig.ac.jp/|DDBJ]], [[http://www.genome.jp/kegg/|KEGG]], [[http://www.ncbi.nlm.nih.gov/|NCBI]], etc.) see web services registries such as [[http://www.biocatalogue.org/|BioCatalogue]], [[http://www.embraceregistry.net/|The Embrace Service Registry]] or [[http://webservices.seekda.com/|seekda]].+A list of Web Services provided by EMBL-EBI follows. For services from other providers (e.g. [[http://www.ddbj.nig.ac.jp/|DDBJ]], [[http://www.genome.jp/kegg/|KEGG]], [[http://www.ncbi.nlm.nih.gov/|NCBI]], etc.) see services registries such as [[http://www.biocatalogue.org/|BioCatalogue]] or [[http://webservices.seekda.com/|seekda]].
==== Data Retrieval ==== ==== Data Retrieval ====
Line 26: Line 26:
^ Service ^ Clients ^ Description ^ ^ Service ^ Clients ^ Description ^
| [[http://www.ebi.ac.uk/fg/doc/help/programmatic_access.html|ArrayExpress]] | | Microarray data searching with [[http://www.ebi.ac.uk/arrayexpress/|ArrayExpress]]. | | [[http://www.ebi.ac.uk/fg/doc/help/programmatic_access.html|ArrayExpress]] | | Microarray data searching with [[http://www.ebi.ac.uk/arrayexpress/|ArrayExpress]]. |
-| [[http://www.ebi.ac.uk/chebi/webServices.do|ChEBI Web Services]] | [[http://www.ebi.ac.uk/chebi/webServices.do#SOAP%20Clients|ChEBI Web Services]] | Entry retrieval from the [[http://www.ebi.ac.uk/chebi/|ChEBI]] database. | +| [[http://www.ebi.ac.uk/chebi/webServices.do|ChEBI Web Services]] | [[http://www.ebi.ac.uk/chebi/webServices.do#4.%20SOAP%20Clients|ChEBI Web Services]] | Entry retrieval from the [[http://www.ebi.ac.uk/chebi/|ChEBI]] database.
-| [[services:eb-eye|EB-Eye]] | [[services:eb-eye#clients|EB-eye]] | Database search using the [[http://www.ebi.ac.uk/inc/help/search_help.html|EB-eye]] search engine. |+| [[https://www.ebi.ac.uk/chembldb/index.php/ws|ChEMBL Web Services]] | [[https://www.ebi.ac.uk/chembldb/index.php/ws|ChEMBL Web Services]] | Search data in, and retrieve data from the [[https://www.ebi.ac.uk/chembldb/|ChEMBL]] database
 +| [[services:eb-eye|EB-eye (SOAP)]] | [[services:eb-eye#clients|EB-eye (SOAP)]] | Database search using the [[http://www.ebi.ac.uk/ebisearch/|EBI Search]] search engine (EB-eye).
 +| [[services:eb-eye_rest|EB-eye (REST)]] | [[services:eb-eye_rest#clients|EB-eye (REST)]] | Database search using the [[http://www.ebi.ac.uk/ebisearch/|EBI Search]] search engine (EB-eye). |
| [[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/~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/rhea/rest/1.0/|Rhea]] | | Manually annotated database of chemical reactions |
| [[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. |
Line 40: Line 41:
==== Analysis Tools ==== ==== Analysis Tools ====
-^ Service ^ Clients ^ Description ^ +^ REST Service ^ SOAP Service ^ Description ^ 
-| [[soaplab:overview|Soaplab]] | [[soaplab:guide|examples]] | Includes most EMBOSS applications that are suitable for launching through Web Services | +| [[:services:so:CENSOR (REST)]] | [[:services:so:CENSOR (SOAP)]] | Identify and/or mask repeat sequences in protein or nucleotide sequence data |
-| [[services:censor|WSCensor]] | [[services:censor#clients|WSCensor]] | A tool which screens query sequences against a reference collection of repeats |+
==== Protein Functional Analysis (PFA) ==== ==== Protein Functional Analysis (PFA) ====
^ 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:iprscan5_rest|InterProScan 5 (REST)]] | [[:services:pfa:iprscan5_soap|InterProScan 5 (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:PfamScan (REST)]] | [[:services:pfa:Pfamscan (SOAP)]] | PfamScan is used to search a FASTA sequence against a library of Pfam HMM. | 
 +| [[: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 ^
Line 62: Line 69:
==== 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 ^
Line 80: Line 89:
==== Pairwise Sequence Alignment (PSA) ==== ==== Pairwise Sequence Alignment (PSA) ====
 +
 +Alignment of two sequences.
^ REST Service ^ SOAP Service ^ Description ^ ^ REST Service ^ SOAP Service ^ Description ^
Line 90: Line 101:
| [[:services:psa:PromoterWise (REST)]]  | [[:services:psa:PromoterWise (SOAP)]]  | Comparing two DNA sequences allowing for inversions and translocations, ideal for promoters. | | [[:services:psa:PromoterWise (REST)]]  | [[:services:psa:PromoterWise (SOAP)]]  | Comparing two DNA sequences allowing for inversions and translocations, ideal for promoters. |
| [[:services:psa:Wise2DBA (REST)]]  | [[:services:psa:Wise2DBA (SOAP)]]  | The Wise2 DNA Block Aligner (DBA) aligns two DNA sequences. | | [[:services:psa:Wise2DBA (REST)]]  | [[:services:psa:Wise2DBA (SOAP)]]  | The Wise2 DNA Block Aligner (DBA) aligns two DNA sequences. |
 +
 +
 +==== RNA ====
 +
 +RNA Anslysis
 +
 +^ REST Service ^ SOAP Service ^ Description ^
 +| [[:services:rna:Infernal cmscan (REST)]]  | [[:services:rna:Infernal cmscan(SOAP)]]  | Infernal cmscan is used to search the CM-format Rfam database. |
 +| [[:services:rna:MapMi (REST)]]  | [[:services:rna:MapMi (SOAP)]]  | Mapping and analysis of miRNA sequences. |
==== 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 ^
Line 99: Line 121:
==== 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. |
Line 107: Line 133:
==== 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 ^
Line 115: Line 143:
==== Structural Analysis ==== ==== Structural Analysis ====
 +
 +Analysis of macromolecular structures.
^ REST Service ^ SOAP Service ^ Description ^ ^ REST Service ^ SOAP Service ^ Description ^
| [[:services:structure:DaliLite (REST)]]  | [[:services:structure:DaliLite (SOAP)]]  | Pairwise structure comparison.  | | [[:services:structure:DaliLite (REST)]]  | [[:services:structure:DaliLite (SOAP)]]  | Pairwise structure comparison.  |
| [[:services:structure:MaxSprout (REST)]]  | [[:services:structure:MaxSprout (SOAP)]]  | Fast database algorithm for generating protein backbone and side chain co-ordinates from a C(alpha) trace. | | [[:services:structure:MaxSprout (REST)]]  | [[:services:structure:MaxSprout (SOAP)]]  | Fast database algorithm for generating protein backbone and side chain co-ordinates from a C(alpha) trace. |
-|  | [[services:dalilite|WSDaliLite]] | Pairwise structure comparison | 
-|  | [[services:maxsprout|WSMaxSprout]]  | Fast database algorithm for generating protein backbone and side chain co-ordinates from a C(alpha) trace  | 
==== Literature and Ontologies ==== ==== Literature and Ontologies ====
 +
 +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://www.ebi.ac.uk/citexplore/webservice.jsp|WSCiteXplore]] | [[clients:citexplore|WSCiteXplore]] | Search the [[http://www.ebi.ac.uk/citexplore/|CiteXplore]] citation database |+| [[http://europepmc.org/WebServices|Europe PMC Web Service]] | | Search [[http://europepmc.org/|Europe PubMed Central]] |
| [[http://www.ebi.ac.uk/miriam/#webservices|WSMIRIAM]] | | Web Services for the Minimal Information Requested In the Annotation of biochemical Models (MIRIAM) | | [[http://www.ebi.ac.uk/miriam/#webservices|WSMIRIAM]] | | Web Services for the Minimal Information Requested In the Annotation of biochemical Models (MIRIAM) |
| [[http://www.ebi.ac.uk/ontology-lookup/WSDLDocumentation.do|WSOntology Lookup]] | | Search multiple ontologies from a single location with a unified output format | | [[http://www.ebi.ac.uk/ontology-lookup/WSDLDocumentation.do|WSOntology Lookup]] | | Search multiple ontologies from a single location with a unified output format |
 
about/webservices.1347358209.txt · Last modified: 2012/09/11 11:10 by hpm
spacer
spacer