{"id":641,"date":"2021-04-20T15:34:48","date_gmt":"2021-04-20T15:34:48","guid":{"rendered":"https:\/\/www.ebi.ac.uk\/about\/clusters\/technical-services\/?p=641"},"modified":"2021-04-20T15:34:48","modified_gmt":"2021-04-20T15:34:48","slug":"a-search-engine-for-the-life-sciences","status":"publish","type":"post","link":"https:\/\/www.ebi.ac.uk\/about\/teams\/its\/blog\/2021\/04\/a-search-engine-for-the-life-sciences\/","title":{"rendered":"A search engine for the life sciences"},"content":{"rendered":"\n
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EMBL-EBI makes a vast quantity of biological data freely available to the global scientific community, via a number of online archives and analysis platforms. For all this data to be useful, the user needs to be able to find what they’re looking for logically, quickly and easily. To do this, advanced, bespoke search functionality is required, and this is where EBI Search comes in\u2026.<\/p>\n\n\n\n\n\n\n\n

Non-traditional IT<\/strong><\/h3>\n\n\n\n

EBI Search<\/a> was first conceived of in 2006, during a discussion initiated by the then directors of EMBL-EBI regarding the increasingly complex search requirements of the institute\u2019s growing data infrastructure. One of those present was Rodrigo Lopez, still the head of EMBL-EBI\u2019s Web Production team to this day (\u201cI almost resigned!\u201d he chuckles). <\/p>\n\n\n\n

What they\nwere describing was a massive undertaking: an engine capable of cross\nreferencing data sources in a way that no \u2018off-the-shelf\u2019 system could handle.\nIt would need to be constructed in-house, from the ground up, and the effort\nand time required would be monumental\u2026 And so, \u201cEB-eye\u201d (its name later changed\nto the more palatable “EBI Search”), was born. <\/p>\n\n\n\n

\u201cThis is not\ntraditional IT,\u201d says Rodrigo. \u201cEBI Search is very powerful, capable and\nscalable, in a way that most search engines are not.\u201d Most notably, it possesses\nthe ability to cross reference results, so in addition to simply displaying the\nresults based on your chosen search criteria, it also shows how these results\nmight relate to each other, and, consequently, what other data might be\nrelevant. <\/p>\n\n\n\n

Over 3 billion documents<\/strong><\/h3>\n\n\n\n

This\n\u2018one-to-many\u2019 relationship is crucial to enabling users to discover new data\nrelevant to their research. Rodrigo explains: \u201cif we know there is a\nrelationship between two points: A and B, we automatically infer a relationship\nbetween B and A, so you can search in a bidirectional way across the data. If B\nhas a relationship with C, then there is also an inferred relationship between\nA and C. Imagine a galactic explosion of points in the sky that represent each\nof these relationships. Our search system actually shows that.\u201d<\/p>\n\n\n\n

Indexing\nover 3 billion documents, this gigantic graph of cross references is thought to\nbe several trillion nodes large, and growing on a daily basis. The richness of\nthe data presents its own problems too. It can be anything: XML, images,\nstructured data, text files, JSON, etc, and EBI Search must index it\nregardless. Equally, the data could be tiny in size \u2014 just a string of letters\nrepresenting a genetic sequence \u2014 all the way up to a large collection of high\nresolution images, numbering many terabytes. <\/p>\n\n\n\n

Opening up COVID-19 data<\/strong><\/h3>\n\n\n\n

The value\nand importance of EBI Search was put to the test recently when EMBL-EBI, with\nfunding from the European Commission, created the COVID-19 Data Portal<\/a>, which is used by researchers\nall over the world studying the disease. After a massive cross-institute effort\ninvolving numerous teams and individuals (including the Web Production and Web\nDevelopment teams from the Technical\nServices Cluster<\/a>), the portal was operational in just two weeks. \u201cPersonally, I was very\nexcited to take part in this project\u201d, says the EBI Search Technical Project\nLead, Youngmi Park, \u201cwe all understand the seriousness of the topic and the\nimportance of the portal, and I have been very impressed by the collaboration\nbetween the teams\u201d.<\/p>\n\n\n\n

Critical to the portal\u2019s success is the functionality of EBI Search, enabling all SARS-CoV-2 and COVID-19 related data to be indexed independently and accessed via the portal. The technological infrastructure that enables researchers everywhere to access, share and analyse these data is crucial in the race to understand the virus and identify viable treatments and vaccines. \u201cThe great thing about working here is that you’re not just fitting hard drives or writing code,\u201d says Rodrigo. \u201cWhat you\u2019re doing has the potential to save lives.\u201d<\/p>\n","protected":false},"excerpt":{"rendered":"

EMBL-EBI makes a vast quantity of biological data freely available to the global scientific community, via a number of online archives and analysis platforms. For all this data to be useful, the user needs to be able to find what they’re looking for logically, quickly and easily. To do this,…<\/p>\n","protected":false},"author":3,"featured_media":0,"comment_status":"closed","ping_status":"closed","sticky":false,"template":"","format":"standard","meta":{"_acf_changed":false,"footnotes":""},"categories":[4002],"tags":[2059,4003,4004,4005],"embl_taxonomy":[],"class_list":["post-641","post","type-post","status-publish","format-standard","hentry","category-search","tag-bioinformatics","tag-covid-19","tag-search","tag-search-engine"],"acf":[],"embl_taxonomy_terms":[],"featured_image_src":"https:\/\/www.ebi.ac.uk\/about\/teams\/its\/wp-includes\/images\/media\/default.svg","_links":{"self":[{"href":"https:\/\/www.ebi.ac.uk\/about\/teams\/its\/wp-json\/wp\/v2\/posts\/641","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/www.ebi.ac.uk\/about\/teams\/its\/wp-json\/wp\/v2\/posts"}],"about":[{"href":"https:\/\/www.ebi.ac.uk\/about\/teams\/its\/wp-json\/wp\/v2\/types\/post"}],"author":[{"embeddable":true,"href":"https:\/\/www.ebi.ac.uk\/about\/teams\/its\/wp-json\/wp\/v2\/users\/3"}],"replies":[{"embeddable":true,"href":"https:\/\/www.ebi.ac.uk\/about\/teams\/its\/wp-json\/wp\/v2\/comments?post=641"}],"version-history":[{"count":1,"href":"https:\/\/www.ebi.ac.uk\/about\/teams\/its\/wp-json\/wp\/v2\/posts\/641\/revisions"}],"predecessor-version":[{"id":643,"href":"https:\/\/www.ebi.ac.uk\/about\/teams\/its\/wp-json\/wp\/v2\/posts\/641\/revisions\/643"}],"wp:attachment":[{"href":"https:\/\/www.ebi.ac.uk\/about\/teams\/its\/wp-json\/wp\/v2\/media?parent=641"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"https:\/\/www.ebi.ac.uk\/about\/teams\/its\/wp-json\/wp\/v2\/categories?post=641"},{"taxonomy":"post_tag","embeddable":true,"href":"https:\/\/www.ebi.ac.uk\/about\/teams\/its\/wp-json\/wp\/v2\/tags?post=641"},{"taxonomy":"embl_taxonomy","embeddable":true,"href":"https:\/\/www.ebi.ac.uk\/about\/teams\/its\/wp-json\/wp\/v2\/embl_taxonomy?post=641"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}