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about:webservices [2013/03/06 09:55]
wli (172.22.69.114)
about:webservices [2016/11/03 13:06] (current)
apc (10.7.243.31)
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===== Introduction ===== ===== Introduction =====
-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 
 +((Li W, Cowley A, Uludag M, Gur T, McWilliam H, Squizzato S, Park YM, Buso N, Lopez R. (2015)\\ 
 +**The EMBL-EBI bioinformatics web and programmatic tools framework.**\\ 
 +Nucleic Acids Res. \\ 
 +PubMed: [[http://europepmc.org/abstract/MED/25845596|25845596]]\\  
 +DOI: [[http://dx.doi.org/10.1093/nar/gkv279|10.1093/nar/gkv279]])) 
 +((Lopez R, Cowley A, Li W, McWilliam H. (2014)\\ 
 +**Using EMBL-EBI Services via Web Interface and Programmatically via Web Services.**\\  
 +Curr Protoc Bioinformatics. 2014;48 3.12.1-3.12.50.\\ 
 +PubMed: [[http://europepmc.org/abstract/MED/25501941|25501941]]\\  
 +DOI: [[http://dx.doi.org/10.1002/0471250953.bi0312s48|10.1002/0471250953.bi0312s485]])).
-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]].
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===== 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 ====
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^ 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. |
| [[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 | | [[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]] | [[services:eb-eye#clients|EB-eye]] | Database search using the [[http://www.ebi.ac.uk/inc/help/search_help.html|EB-eye]] search engine. |+| [[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.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://www.ebi.ac.uk/pdbe/pdbe-rest-api|PDBe (REST)]] | | PDBe’s REST API is a programmatic way to obtain information from the PDB and EMDB. |
| [[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.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. |
| [[services:dbfetch|WSDbfetch (SOAP)]] | [[services:dbfetch#clients|WSDbfetch (SOAP)]] | Identifier based entry retrieval for various up-to-date biological databases. | | [[services:dbfetch|WSDbfetch (SOAP)]] | [[services:dbfetch#clients|WSDbfetch (SOAP)]] | Identifier based entry retrieval for various up-to-date biological databases. |
-==== Analysis Tools ==== 
-^ REST Service ^ SOAP Service ^ Description ^ 
-| [[:services:so:CENSOR (REST)]] | [[:services:so:CENSOR (SOAP)]] | Identify and/or mask repeat sequences in protein or nucleotide sequence data | 
==== Protein Functional Analysis (PFA) ==== ==== Protein Functional Analysis (PFA) ====
^ REST Service ^ SOAP Service ^ Description ^ ^ REST Service ^ SOAP Service ^ Description ^
-| [[:services:pfa:FingerPRINTScan (REST)]] | [[:services:pfa:FingerPRINTScan(SOAP)]] | Identifying the closest matching PRINTS sequence motif fingerprints in a protein sequence | +| [[:services:pfa:FingerPRINTScan (REST)]] | [[:services:pfa:FingerPRINTScan(SOAP)]] | Identifying the closest matching PRINTS sequence motif fingerprints in a protein sequence.
-| [[:services:pfa:iprscan_rest|InterProScan (REST)]] | [[:services:pfa:iprscan_soap|InterProScan (SOAP)]] | A tool that combines different protein signature recognition methods. | +| [[: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:Phobius (REST)]] | [[:services:pfa:Phobius (SOAP)]] | Prediction of transmembrane topology and signal peptides from the amino acid sequence of a protein | +| [[: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:Pratt (REST)]] | [[:services:pfa:Pratt (SOAP)]] | Searching for patterns conserved in sets of unaligned protein sequences | +| [[:services:pfa:PfamScan (REST)]] | [[:services:pfa:Pfamscan (SOAP)]] | PfamScan is used to search a FASTA sequence against a library of Pfam HMM. | 
-| [[: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 |+| [[: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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| [[services:sss:psiblast_rest|PSI-BLAST (REST)]] | [[services:sss:psiblast_soap|PSI-BLAST (SOAP)]] | Position Specific Iterative BLAST (PSI-BLAST), guided mode | | [[services:sss:psiblast_rest|PSI-BLAST (REST)]] | [[services:sss:psiblast_soap|PSI-BLAST (SOAP)]] | Position Specific Iterative BLAST (PSI-BLAST), guided mode |
| [[services:sss:psisearch_rest|PSI-Search (REST)]] | [[services:sss:psisearch_soap|PSI-Search (SOAP)]] | Iterative Smith and Waterman using a PSI-BLAST strategy | | [[services:sss:psisearch_rest|PSI-Search (REST)]] | [[services:sss:psisearch_soap|PSI-Search (SOAP)]] | Iterative Smith and Waterman using a PSI-BLAST strategy |
-| [[services:sss:wu_blast_rest|WU-BLAST (REST)]] | [[services:sss:wu_blast_soap|WU-BLAST (SOAP)]] | Compare a novel sequence with those contained in nucleotide and protein databases using WU-BLAST |+| [[http://http://www.ebi.ac.uk/Tools/hmmer/help/api|HMMER (REST)]] | | Fast, sensitive search using HMMER suite. Includes phmmer, hmmscan, hmmsearch and jackhmmer | 
==== 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 ^
| [[services:msa:clustalo_rest|Clustal Omega (REST)]] | [[services:msa:clustalo_soap|Clustal Omega (SOAP)]] | Protein, DNA and RNA multiple sequence alignment using Clustal Omega. | | [[services:msa:clustalo_rest|Clustal Omega (REST)]] | [[services:msa:clustalo_soap|Clustal Omega (SOAP)]] | Protein, DNA and RNA multiple sequence alignment using Clustal Omega. |
-| [[services:msa:ClustalW2 (REST)]] | [[services:msa:ClustalW2 (SOAP)]] | Global multiple sequence alignment of DNA and protein sequences using ClustalW 2. +| [[services:msa:ClustalW2 (REST)]] | [[services:msa:ClustalW2 (SOAP)]] | **SERVICE RETIRED** 
-| [[:services:msa:DbClustal (REST)]] | [[:services:msa:DbClustal (SOAP)]] | Global multiple sequence alignment of DNA or protein sequences using anchor regions from BLAST results |+| [[:services:msa:DbClustal (REST)]] | [[:services:msa:DbClustal (SOAP)]] | **SERVICE RETIRED** |
| [[services:msa:Kalign (REST)]]      | [[services:msa:Kalign (SOAP)]] | Sequence alignment using the Kalign method. Fast and accurate algorithm, which handles large sequences. | | [[services:msa:Kalign (REST)]]      | [[services:msa:Kalign (SOAP)]] | Sequence alignment using the Kalign method. Fast and accurate algorithm, which handles large sequences. |
| [[services:msa:MAFFT (REST)]]        | [[services:msa:MAFFT (SOAP)]] | Sequence alignment using the MAFFT method. Fast and capable of handling large sequences. | | [[services:msa:MAFFT (REST)]]        | [[services:msa:MAFFT (SOAP)]] | Sequence alignment using the MAFFT method. Fast and capable of handling large sequences. |
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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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| [[: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 ^
| [[:services:sfc:EMBOSS seqret (REST)]]  | [[:services:sfc:EMBOSS seqret (SOAP)]]  | Manipulation of sequence entries, including conversion between sequence data formats.  | | [[:services:sfc:EMBOSS seqret (REST)]]  | [[:services:sfc:EMBOSS seqret (SOAP)]]  | Manipulation of sequence entries, including conversion between sequence data formats.  |
| [[:services:msa:MView (REST)]]  | [[:services:msa:MView (SOAP)]]  | Reformatting of multiple sequence alignment data.  | | [[:services:msa:MView (REST)]]  | [[:services:msa:MView (SOAP)]]  | Reformatting of multiple sequence alignment data.  |
-| [[:services:sfc:Readseq (REST)]]  | [[:services:sfc:Readseq (SOAP)]]  | Convert biosequences between a selection of common biological sequence formats.  |+| [[:services:sfc:Readseq (REST)]]  | [[:services:sfc:Readseq (SOAP)]]  | **SERVICE RETIRED** |
==== 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 ^
-| [[:services:structure:DaliLite (REST)]]  | [[:services:structure:DaliLite (SOAP)]]  | Pairwise structure comparison.  +| [[:services:structure:DaliLite (REST)]]  | [[:services:structure:DaliLite (SOAP)]]  | **SERVICE RETIRED** 
-| [[: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)]]  | **SERVICE RETIRED**  |
==== 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 ^
 
about/webservices.1362563726.txt · Last modified: 2013/03/06 09:55 (external edit)
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