The EMBL-EBI search and sequence analysis tools APIs in 2019

被引：3175

作者：

Madeira, Fabio ^{[1
]}

Park, Young Mi ^{[1
]}

Lee, Joon ^{[1
]}

Buso, Nicola ^{[1
]}

Gur, Tamer ^{[1
]}

Madhusoodanan, Nandana ^{[1
]}

Basutkar, Prasad ^{[1
]}

Tivey, Adrian R. N. ^{[1
]}

Potter, Simon C. ^{[1
]}

Finn, Robert D. ^{[1
]}

Lopez, Rodrigo ^{[1
]}

机构：

[1] EBI, EMBL, Wellcome Trust Genome Campus, Cambridge CB10 1SD, England

来源：

NUCLEIC ACIDS RESEARCH | 2019年 / 47卷 / W1期

基金：

欧盟地平线“2020”;

关键词：

DATABASE; PERFORMANCE; DISCOVERY;

D O I：

10.1093/nar/gkz268

中图分类号：

Q5 [生物化学]; Q7 [分子生物学];

学科分类号：

071010 ; 081704 ;

摘要：

The EMBL-EBI provides free access to popular bioinformatics sequence analysis applications as well as to a full-featured text search engine with powerful cross-referencing and data retrieval capabilities. Access to these services is provided via user-friendly web interfaces and via established RESTful and SOAP Web Services APIs (https://www.ebi.ac.uk/seqdb/confluence/display/JDSAT/EMBL-EBI+Web+Services+APIs+-+Data+Retrieval). Both systems have been developed with the same core principles that allow them to integrate an ever-increasing volume of biological data, making them an integral part of many popular data resources provided at the EMBL-EBI. Here, we describe the latest improvements made to the frameworks which enhance the interconnectivity between public EMBL-EBI resources and ultimately enhance biological data discoverability, accessibility, interoperability and reusability.

引用

页码：W636 / W641

页数：6

共 34 条

[1]

Amstutz P., 2016, Common workflow language,, DOI 10.6084/m9.figshare.3115156.v2

[2] UniProt: a worldwide hub of protein knowledge [J].

Bateman, Alex ;

Martin, Maria-Jesus ;

Orchard, Sandra ;

Magrane, Michele ;

Alpi, Emanuele ;

Bely, Benoit ;

Bingley, Mark ;

Britto, Ramona ;

Bursteinas, Borisas ;

Busiello, Gianluca ;

Bye-A-Jee, Hema ;

Da Silva, Alan ;

De Giorgi, Maurizio ;

Dogan, Tunca ;

Castro, Leyla Garcia ;

Garmiri, Penelope ;

Georghiou, George ;

Gonzales, Daniel ;

Gonzales, Leonardo ;

Hatton-Ellis, Emma ;

Ignatchenko, Alexandr ;

Ishtiaq, Rizwan ;

Jokinen, Petteri ;

Joshi, Vishal ;

Jyothi, Dushyanth ;

Lopez, Rodrigo ;

Luo, Jie ;

Lussi, Yvonne ;

MacDougall, Alistair ;

Madeira, Fabio ;

Mahmoudy, Mahdi ;

Menchi, Manuela ;

Nightingale, Andrew ;

Onwubiko, Joseph ;

Palka, Barbara ;

Pichler, Klemens ;

Pundir, Sangya ;

Qi, Guoying ;

Raj, Shriya ;

Renaux, Alexandre ;

Lopez, Milagros Rodriguez ;

Saidi, Rabie ;

Sawford, Tony ;

Shypitsyna, Aleksandra ;

Speretta, Elena ;

Turner, Edward ;

Tyagi, Nidhi ;

Vasudev, Preethi ;

Volynkin, Vladimir ;

Wardell, Tony .

NUCLEIC ACIDS RESEARCH, 2019, 47 (D1) :D506-D515

[3] Performance, Accuracy, and Web Server for Evolutionary Placement of Short Sequence Reads under Maximum Likelihood [J].

Berger, Simon A. ;

Krompass, Denis ;

Stamatakis, Alexandros .

SYSTEMATIC BIOLOGY, 2011, 60 (03) :291-302

[4] Protein Data Bank: the single global archive for 3D macromolecular structure data [J].

Burley, Stephen K. ;

Berman, Helen M. ;

Bhikadiya, Charmi ;

Bi, Chunxiao ;

Chen, Li ;

Di Costanzo, Luigi ;

Christie, Cole ;

Duarte, Jose M. ;

Dutta, Shuchismita ;

Feng, Zukang ;

Ghosh, Sutapa ;

Goodsell, David S. ;

Green, Rachel Kramer ;

Guranovic, Vladimir ;

Guzenko, Dmytro ;

Hudson, Brian P. ;

Liang, Yuhe ;

Lowe, Robert ;

Peisach, Ezra ;

Periskova, Irina ;

Randle, Chris ;

Rose, Alexander ;

Sekharan, Monica ;

Shao, Chenghua ;

Tao, Yi-Ping ;

Valasatava, Yana ;

Voigt, Maria ;

Westbrook, John ;

Young, Jasmine ;

Zardecki, Christine ;

Zhuravleva, Marina ;

Kurisu, Genji ;

Nakamura, Haruki ;

Kengaku, Yumiko ;

Cho, Hasumi ;

Sato, Junko ;

Kim, Ju Yaen ;

Ikegawa, Yasuyo ;

Nakagawa, Atsushi ;

Yamashita, Reiko ;

Kudou, Takahiro ;

Bekker, Gert-Jan ;

Suzuki, Hirofumi ;

Iwata, Takeshi ;

Yokochi, Masashi ;

Kobayashi, Naohiro ;

Fujiwara, Toshimichi ;

Velankar, Sameer ;

Kleywegt, Gerard J. ;

Anyango, Stephen .

NUCLEIC ACIDS RESEARCH, 2019, 47 (D1) :D520-D528

[5] BLAST plus : architecture and applications [J].

Camacho, Christiam ;

Coulouris, George ;

Avagyan, Vahram ;

Ma, Ning ;

Papadopoulos, Jason ;

Bealer, Kevin ;

Madden, Thomas L. .

BMC BIOINFORMATICS, 2009, 10

[6] Programmatic access to bioinformatics tools from EMBL-EBI update: 2017 [J].

Chojnacki, Szymon ;

Cowley, Andrew ;

Lee, Joon ;

Foix, Anna ;

Lopez, Rodrigo .

NUCLEIC ACIDS RESEARCH, 2017, 45 (W1) :W550-W553

[7] The European Bioinformatics Institute in 2016: Data growth and integration [J].

Cook, Charles E. ;

Bergman, Mary Todd ;

Finn, Robert D. ;

Cochrane, Guy ;

Birney, Ewan ;

Apweiler, Rolf .

NUCLEIC ACIDS RESEARCH, 2016, 44 (D1) :D20-D26

[8] SIFTS: updated Structure Integration with Function, Taxonomy and Sequences resource allows 40-fold increase in coverage of structure-based annotations for proteins [J].

Dana, Jose M. ;

Gutmanas, Aleksandras ;

Tyagi, Nidhi ;

Qi, Guoying ;

O'Donovan, Claire ;

Martin, Maria ;

Velankar, Sameer .

NUCLEIC ACIDS RESEARCH, 2019, 47 (D1) :D482-D489

[9] ScanProsite: detection of PROSITE signature matches and ProRule-associated functional and structural residues in proteins [J].

de Castro, Edouard ;

Sigrist, Christian J. A. ;

Gattiker, Alexandre ;

Bulliard, Virginie ;

Langendijk-Genevaux, Petra S. ;

Gasteiger, Elisabeth ;

Bairoch, Amos ;

Hulo, Nicolas .

NUCLEIC ACIDS RESEARCH, 2006, 34 :W362-W365

[10] The discovery, positioning and verification of a set of transcription-associated motifs in vertebrates [J].

Ettwiller, L ;

Paten, B ;

Souren, M ;

Loosli, F ;

Wittbrodt, J ;

Birney, E .

GENOME BIOLOGY, 2005, 6 (12)

← 1 2 3 4 →