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about:webservices [2014/06/30 10:59]
ympark (172.22.68.30)
about:webservices [2017/07/10 19:07] (current)
rls (82.13.79.12)
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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 
 +((Chojnacki S,  Cowley A,  Lee J,  Foix A,  Lopez R. (2017)\\   
 +**Programmatic access to bioinformatics tools from EMBL-EBI update: 2017.**\\ 
 +Nucleic Acids Res. \\ 
 +PubMed: [[http://europepmc.org/abstract/MED/28431173|28431173]]\\ 
 +DOI: [[https://doi.org/10.1093/nar/gkx273|10.1093/nar/gkx273]])) 
 +((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:
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===== Important Note ===== ===== Important Note =====
 +**We kindly ask all users of EMBL-EBI Web Services to submit tool jobs in batches of no more than 30 at a time and not to submit more until the results and processing is complete. Please ensure that a valid email address is provided. Excessive usage of a particular resource will be dealt with in accordance with [[http://www.ebi.ac.uk/about/terms-of-use|EMBL-EBI's Terms of Use]].
-**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.**+ 
 +Please [[https://www.ebi.ac.uk/support/webservices|contact us]] if you need further information.** 
 + 
 +---- 
 +Chinese / 中文 
 + 
 +敬告所有 EMBL-EBI Web Services 网络服务用户,请在呈交工具工作时,每批工作 不要超过30项,并请您在该批数据的结果和处理程序完成之后再呈交下一批工作。并请您提供一个有效的电子邮件地址。超额使用某项资源将按照 [[http://www.ebi.ac.uk/about/terms-of-use|EMBL-EBI使用条款处理。]]  如需进一步信息,请通过此链接 [[https://www.ebi.ac.uk/support/webservices| 与我们联系。]] 
 + 
 +---- 
 + 
 +Korean / 한글 
 + 
 +EMBL-EBI 웹서비스는 다량의 데이터(배치 등) 호출시, 사용자당 실시간으로 최대 30건의 처리를 제한적으로 사용하실 것을 권고드리고 있습니다. 보내신 건이 완료되기 전에, 재차 더 많은 데이터가 전송되지 않도록 협조 부탁드립니다. 또한 유효한 메일주소를 사용해주시기 바랍니다. 다량의 데이터 사용에 관한, [[http://www.ebi.ac.uk/about/terms-of-use|EMBL-EBI 이용 약관]]을  준수해 주시것을 부탁드리며, 관련해 도움이 필요하시면, [[https://www.ebi.ac.uk/support/webservices|문의]] 주시기 바랍니다.
===== 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 services registries such as [[http://www.biocatalogue.org/|BioCatalogue]] 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]].
==== Data Retrieval ==== ==== Data Retrieval ====
^ 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]]. |+| [[https://www.ebi.ac.uk/arrayexpress/help/programmatic_access.html|Array Express]] | | 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#4.%20SOAP%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 (SOAP)]] | [[services:eb-eye#clients|EB-eye (SOAP)]] | Database search using the [[http://www.ebi.ac.uk/ebisearch/|EBI Search]] search engine (EB-eye). | +| [[http://www.ebi.ac.uk/ebisearch/swagger.ebi|EBI Search (formerly EB-eye)]] | [[http://www.ebi.ac.uk/ebisearch/swagger.ebi#sample_clients|EBI Search (formerly EB-eye)]] | 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 |+| [[https://www.ebi.ac.uk/gxa/FAQ.html#api|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://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/pdbe/pdbe-rest-api|PDBe (REST)]] | | PDBe’s REST API is a programmatic way to obtain information from the PDB and EMDB. | 
 +| [[https://github.com/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.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. |
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| [[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:iprscan5_rest|InterProScan 5 (REST)]] | [[:services:pfa:iprscan5_soap|InterProScan 5 (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: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: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. |
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| [[: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: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: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. |
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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 |+| [[https://hmmer-web-docs.readthedocs.io/en/latest/api.html|HMMER (REST)]] | | Fast, sensitive search using HMMER suite. Includes phmmer, hmmscan, hmmsearch and jackhmmer | 
==== Multiple Sequence Alignment (MSA) ==== ==== Multiple Sequence Alignment (MSA) ====
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^ 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:DbClustal (REST)]] | [[:services:msa:DbClustal (SOAP)]] | Global multiple sequence alignment of DNA or protein sequences using anchor regions from BLAST results | 
| [[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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^ REST Service ^ SOAP Service ^ Description ^ ^ REST Service ^ SOAP Service ^ Description ^
-| [[services:phylogeny:ClustalW2 Phylogeny (REST)]] | [[services:phylogeny:ClustalW2 Phylogeny (SOAP)]] | Neighbor-joining or UPGMA phylogenetic trees from an alignment using ClustalW 2. |+| [[services:phylogeny:Simple Phylogeny (REST)]] | [[services:phylogeny:Simple Phylogeny (SOAP)]] | Neighbor-joining or UPGMA phylogenetic trees from an alignment using ClustalW2. |
==== Pairwise Sequence Alignment (PSA) ==== ==== Pairwise Sequence Alignment (PSA) ====
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==== RNA ==== ==== RNA ====
-RNA Anslysis+RNA Analysis
^ REST Service ^ SOAP Service ^ Description ^ ^ REST Service ^ SOAP Service ^ Description ^
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| [[: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.  | 
==== Sequence Statistics ==== ==== Sequence Statistics ====
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| [[:services:st:EMBOSS backtranambig (REST)]]  | [[:services:st:EMBOSS backtranambig (SOAP)]]  | EMBOSS backtranambig back-translates protein sequences to ambiguous nucleotide sequences. | | [[:services:st:EMBOSS backtranambig (REST)]]  | [[:services:st:EMBOSS backtranambig (SOAP)]]  | EMBOSS backtranambig back-translates protein sequences to ambiguous nucleotide sequences. |
-==== Structural Analysis ==== 
-Analysis of macromolecular structures. 
- 
-^ REST Service ^ SOAP Service ^ Description ^ 
-| [[: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. | 
==== Literature and Ontologies ==== ==== Literature and Ontologies ====
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| [[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]] |
| [[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 |+| [[https://www.ebi.ac.uk/ols/docs/api|Ontology Lookup Service API]] | | Search multiple ontologies from a single location with a unified output format |
| [[http://www.ebi.ac.uk/sbo/SBOWSLib/ws.html|WSSBO]] | [[http://www.ebi.ac.uk/sbo/SBOWSLib/ws.html|WSSBO]] | Web Services for the Systems Biology Ontology (SBO) | | [[http://www.ebi.ac.uk/sbo/SBOWSLib/ws.html|WSSBO]] | [[http://www.ebi.ac.uk/sbo/SBOWSLib/ws.html|WSSBO]] | Web Services for the Systems Biology Ontology (SBO) |
| [[http://www.ebi.ac.uk/webservices/whatizit/info.jsf|WSWhatizit]] | [[http://www.ebi.ac.uk/webservices/whatizit/helpws.jsp|WSWhatizit]] | A text processing system that allows you to do text mining tasks on text | | [[http://www.ebi.ac.uk/webservices/whatizit/info.jsf|WSWhatizit]] | [[http://www.ebi.ac.uk/webservices/whatizit/helpws.jsp|WSWhatizit]] | A text processing system that allows you to do text mining tasks on text |
 
about/webservices.1404122371.txt · Last modified: 2014/06/30 10:59 by ympark
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