{"id":"https://openalex.org/W4391971691","doi":"https://doi.org/10.1093/bioinformatics/btae095","title":"Fast and scalable querying of eukaryotic linear motifs with <i>gget elm</i>","display_name":"Fast and scalable querying of eukaryotic linear motifs with <i>gget elm</i>","publication_year":2024,"publication_date":"2024-02-19","ids":{"openalex":"https://openalex.org/W4391971691","doi":"https://doi.org/10.1093/bioinformatics/btae095","pmid":"https://pubmed.ncbi.nlm.nih.gov/38377393"},"language":"en","primary_location":{"id":"doi:10.1093/bioinformatics/btae095","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btae095","pdf_url":"https://academic.oup.com/bioinformatics/advance-article-pdf/doi/10.1093/bioinformatics/btae095/56721210/btae095.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","doaj","pubmed"],"open_access":{"is_oa":true,"oa_status":"gold","oa_url":"https://academic.oup.com/bioinformatics/advance-article-pdf/doi/10.1093/bioinformatics/btae095/56721210/btae095.pdf","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5031236248","display_name":"Laura Luebbert","orcid":"https://orcid.org/0000-0003-1379-2927"},"institutions":[{"id":"https://openalex.org/I122411786","display_name":"California Institute of Technology","ror":"https://ror.org/05dxps055","country_code":"US","type":"education","lineage":["https://openalex.org/I122411786"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Laura Luebbert","raw_affiliation_strings":["Division of Biology and Biological Engineering, California Institute of Technology , Pasadena, CA 91125, United States"],"raw_orcid":"https://orcid.org/0000-0003-1379-2927","affiliations":[{"raw_affiliation_string":"Division of Biology and Biological Engineering, California Institute of Technology , Pasadena, CA 91125, United States","institution_ids":["https://openalex.org/I122411786"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5005618787","display_name":"Chi Linh Hoang","orcid":"https://orcid.org/0000-0003-0068-4898"},"institutions":[{"id":"https://openalex.org/I122411786","display_name":"California Institute of Technology","ror":"https://ror.org/05dxps055","country_code":"US","type":"education","lineage":["https://openalex.org/I122411786"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Chi Hoang","raw_affiliation_strings":["California Institute of Technology , Pasadena, CA 91125, United States"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"California Institute of Technology , Pasadena, CA 91125, United States","institution_ids":["https://openalex.org/I122411786"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5047377914","display_name":"Manjeet Kumar","orcid":"https://orcid.org/0000-0002-7146-289X"},"institutions":[{"id":"https://openalex.org/I4210153543","display_name":"European Molecular Biology Laboratory","ror":"https://ror.org/050589e39","country_code":"DE","type":"government","lineage":["https://openalex.org/I4210138560","https://openalex.org/I4210153543"]}],"countries":["DE"],"is_corresponding":false,"raw_author_name":"Manjeet Kumar","raw_affiliation_strings":["Structural and Computational Biology Unit, European Molecular Biology Laboratory (EMBL) , 69117 Heidelberg, Germany"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Structural and Computational Biology Unit, European Molecular Biology Laboratory (EMBL) , 69117 Heidelberg, Germany","institution_ids":["https://openalex.org/I4210153543"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5020008219","display_name":"Lior Pachter","orcid":"https://orcid.org/0000-0002-9164-6231"},"institutions":[{"id":"https://openalex.org/I122411786","display_name":"California Institute of Technology","ror":"https://ror.org/05dxps055","country_code":"US","type":"education","lineage":["https://openalex.org/I122411786"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Lior Pachter","raw_affiliation_strings":["Department of Computing and Mathematical Sciences, California Institute of Technology , Pasadena, CA 91125, United States","Division of Biology and Biological Engineering, California Institute of Technology , Pasadena, CA 91125, United States"],"raw_orcid":"https://orcid.org/0000-0002-9164-6231","affiliations":[{"raw_affiliation_string":"Department of Computing and Mathematical Sciences, California Institute of Technology , Pasadena, CA 91125, United States","institution_ids":["https://openalex.org/I122411786"]},{"raw_affiliation_string":"Division of Biology and Biological Engineering, California Institute of Technology , Pasadena, CA 91125, United States","institution_ids":["https://openalex.org/I122411786"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":4,"corresponding_author_ids":["https://openalex.org/A5020008219"],"corresponding_institution_ids":["https://openalex.org/I122411786"],"apc_list":{"value":3618,"currency":"USD","value_usd":3618},"apc_paid":{"value":3618,"currency":"USD","value_usd":3618},"fwci":0.2016,"has_fulltext":true,"cited_by_count":1,"citation_normalized_percentile":{"value":0.5194171,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":{"min":90,"max":94},"biblio":{"volume":"40","issue":"3","first_page":null,"last_page":null},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10887","display_name":"Bioinformatics and Genomic Networks","score":0.4334000051021576,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},"topics":[{"id":"https://openalex.org/T10887","display_name":"Bioinformatics and Genomic Networks","score":0.4334000051021576,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},{"id":"https://openalex.org/T10044","display_name":"Protein Structure and Dynamics","score":0.17820000648498535,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}},{"id":"https://openalex.org/T12254","display_name":"Machine Learning in Bioinformatics","score":0.0658000037074089,"subfield":{"id":"https://openalex.org/subfields/1312","display_name":"Molecular Biology"},"field":{"id":"https://openalex.org/fields/13","display_name":"Biochemistry, Genetics and Molecular Biology"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/scalability","display_name":"Scalability","score":0.7368322610855103},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.7059410214424133},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.485038697719574},{"id":"https://openalex.org/keywords/theoretical-computer-science","display_name":"Theoretical computer science","score":0.3408958613872528},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.3278962969779968},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.21678566932678223},{"id":"https://openalex.org/keywords/database","display_name":"Database","score":0.17330819368362427}],"concepts":[{"id":"https://openalex.org/C48044578","wikidata":"https://www.wikidata.org/wiki/Q727490","display_name":"Scalability","level":2,"score":0.7368322610855103},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.7059410214424133},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.485038697719574},{"id":"https://openalex.org/C80444323","wikidata":"https://www.wikidata.org/wiki/Q2878974","display_name":"Theoretical computer science","level":1,"score":0.3408958613872528},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.3278962969779968},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.21678566932678223},{"id":"https://openalex.org/C77088390","wikidata":"https://www.wikidata.org/wiki/Q8513","display_name":"Database","level":1,"score":0.17330819368362427}],"mesh":[{"descriptor_ui":"D000595","descriptor_name":"Amino Acid Sequence","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000595","descriptor_name":"Amino Acid Sequence","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000595","descriptor_name":"Amino Acid Sequence","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D000595","descriptor_name":"Amino Acid Sequence","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D011506","descriptor_name":"Proteins","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D012984","descriptor_name":"Software","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D020816","descriptor_name":"Amino Acid Motifs","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020816","descriptor_name":"Amino Acid Motifs","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020816","descriptor_name":"Amino Acid Motifs","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020816","descriptor_name":"Amino Acid Motifs","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D030562","descriptor_name":"Databases, Protein","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D030562","descriptor_name":"Databases, Protein","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D030562","descriptor_name":"Databases, Protein","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D030562","descriptor_name":"Databases, Protein","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false}],"locations_count":3,"locations":[{"id":"doi:10.1093/bioinformatics/btae095","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btae095","pdf_url":"https://academic.oup.com/bioinformatics/advance-article-pdf/doi/10.1093/bioinformatics/btae095/56721210/btae095.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},{"id":"pmid:38377393","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/38377393","pdf_url":null,"source":{"id":"https://openalex.org/S4306525036","display_name":"PubMed","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1299303238","host_organization_name":"National Institutes of Health","host_organization_lineage":["https://openalex.org/I1299303238"],"host_organization_lineage_names":[],"type":"repository"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics (Oxford, England)","raw_type":null},{"id":"pmh:oai:pubmedcentral.nih.gov:10927331","is_oa":true,"landing_page_url":"https://www.ncbi.nlm.nih.gov/pmc/articles/10927331","pdf_url":"https://pmc.ncbi.nlm.nih.gov/articles/PMC10927331/pdf/btae095.pdf","source":{"id":"https://openalex.org/S2764455111","display_name":"PubMed Central","issn_l":null,"issn":null,"is_oa":true,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I1299303238","host_organization_name":"National Institutes of Health","host_organization_lineage":["https://openalex.org/I1299303238"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":"Bioinformatics","raw_type":"Text"}],"best_oa_location":{"id":"doi:10.1093/bioinformatics/btae095","is_oa":true,"landing_page_url":"https://doi.org/10.1093/bioinformatics/btae095","pdf_url":"https://academic.oup.com/bioinformatics/advance-article-pdf/doi/10.1093/bioinformatics/btae095/56721210/btae095.pdf","source":{"id":"https://openalex.org/S52395412","display_name":"Bioinformatics","issn_l":"1367-4803","issn":["1367-4803","1367-4811"],"is_oa":true,"is_in_doaj":true,"is_core":true,"host_organization":"https://openalex.org/P4310311648","host_organization_name":"Oxford University Press","host_organization_lineage":["https://openalex.org/P4310311648","https://openalex.org/P4310311647"],"host_organization_lineage_names":["Oxford University Press","University of Oxford"],"type":"journal"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Bioinformatics","raw_type":"journal-article"},"sustainable_development_goals":[{"display_name":"Partnerships for the goals","id":"https://metadata.un.org/sdg/17","score":0.4399999976158142}],"awards":[],"funders":[{"id":"https://openalex.org/F4320309398","display_name":"California Institute of Technology","ror":"https://ror.org/05dxps055"}],"has_content":{"pdf":true,"grobid_xml":false},"content_urls":{"pdf":"https://content.openalex.org/works/W4391971691.pdf"},"referenced_works_count":31,"referenced_works":["https://openalex.org/W1967721813","https://openalex.org/W2023333666","https://openalex.org/W2110105476","https://openalex.org/W2110336366","https://openalex.org/W2137239190","https://openalex.org/W2143593035","https://openalex.org/W2168514491","https://openalex.org/W2206815873","https://openalex.org/W2330547698","https://openalex.org/W2396441275","https://openalex.org/W2596741751","https://openalex.org/W2767841706","https://openalex.org/W2903068930","https://openalex.org/W2988357750","https://openalex.org/W3017559857","https://openalex.org/W3112376646","https://openalex.org/W3119807775","https://openalex.org/W3143063265","https://openalex.org/W3165745490","https://openalex.org/W3209420441","https://openalex.org/W3212975895","https://openalex.org/W4205989657","https://openalex.org/W4281872574","https://openalex.org/W4296139765","https://openalex.org/W4309845842","https://openalex.org/W4313679372","https://openalex.org/W4313702077","https://openalex.org/W4388668618","https://openalex.org/W6712264756","https://openalex.org/W6756842603","https://openalex.org/W6770400242"],"related_works":["https://openalex.org/W4391375266","https://openalex.org/W2899084033","https://openalex.org/W2748952813","https://openalex.org/W2390279801","https://openalex.org/W4391913857","https://openalex.org/W2358668433","https://openalex.org/W4396701345","https://openalex.org/W2376932109","https://openalex.org/W2001405890","https://openalex.org/W2389214306"],"abstract_inverted_index":{"MOTIVATION:":[0],"Eukaryotic":[1],"linear":[2],"motifs":[3],"(ELMs),":[4],"or":[5,71,101],"Short":[6],"Linear":[7],"Motifs,":[8],"are":[9,25,87,203],"protein":[10,108,122],"interaction":[11,188],"modules":[12],"that":[13],"play":[14],"an":[15],"essential":[16],"role":[17],"in":[18,28,60,89,127,162,178,190],"cellular":[19],"processes":[20],"and":[21,24,56,139,167,182,200],"signaling":[22],"networks":[23],"often":[26],"involved":[27],"diseases":[29],"like":[30],"cancer.":[31],"The":[32,198],"ELM":[33,76,98,129,155,180],"database":[34,181],"is":[35,112],"a":[36,49,144],"collection":[37],"of":[38,93,137],"manually":[39],"curated":[40,126],"motif":[41,54,119],"knowledge":[42],"from":[43],"scientific":[44],"papers.":[45],"It":[46],"has":[47],"become":[48],"crucial":[50],"resource":[51,77],"for":[52,157,186],"investigating":[53],"biology":[55],"recognizing":[57],"candidate":[58,160],"ELMs":[59,125,161],"novel":[61],"amino":[62,68,164,192],"acid":[63,69,165,193],"sequences.":[64,194],"Users":[65],"can":[66],"search":[67],"sequences":[70,123,166],"UniProt":[72,168],"Accessions":[73],"on":[74,121,153],"the":[75,90,97,128,134,154,175,179,191],"web":[78,84,99],"interface.":[79],"However,":[80],"as":[81],"with":[82,143],"many":[83],"services,":[85],"there":[86],"limitations":[88],"swift":[91],"processing":[92],"large-scale":[94,118],"queries":[95],"through":[96],"interface":[100],"API":[102],"calls,":[103],"and,":[104],"therefore,":[105],"integration":[106],"into":[107],"function":[109],"analysis":[110],"pipelines":[111],"limited.":[113],"RESULTS:":[114],"To":[115],"allow":[116],"swift,":[117],"analyses":[120],"using":[124],"database,":[130],"we":[131],"have":[132],"extended":[133],"gget":[135,147,170],"suite":[136],"Python":[138],"command":[140],"line":[141],"tools":[142],"new":[145],"module,":[146],"elm,":[148],"which":[149],"does":[150],"not":[151],"rely":[152],"server":[156],"efficiently":[158],"finding":[159],"user-submitted":[163],"Accessions.":[169],"elm":[171],"increases":[172],"accessibility":[173],"to":[174],"information":[176],"stored":[177],"allows":[183],"scalable":[184],"searches":[185],"motif-mediated":[187],"sites":[189],"AVAILABILITY":[195],"AND":[196],"IMPLEMENTATION:":[197],"manual":[199],"source":[201],"code":[202],"available":[204],"at":[205],"https://github.com/pachterlab/gget.":[206]},"counts_by_year":[{"year":2024,"cited_by_count":1}],"updated_date":"2026-06-16T07:32:37.131356","created_date":"2024-02-21T00:00:00"}