{"id":"https://openalex.org/W4392619347","doi":"https://doi.org/10.1142/s0219720024500057","title":"iCEED: Integrated customized extraction of enzyme data","display_name":"iCEED: Integrated customized extraction of enzyme data","publication_year":2024,"publication_date":"2024-03-09","ids":{"openalex":"https://openalex.org/W4392619347","doi":"https://doi.org/10.1142/s0219720024500057","pmid":"https://pubmed.ncbi.nlm.nih.gov/38779780"},"language":"en","primary_location":{"id":"doi:10.1142/s0219720024500057","is_oa":false,"landing_page_url":"http://dx.doi.org/10.1142/s0219720024500057","pdf_url":null,"source":{"id":"https://openalex.org/S155349577","display_name":"Journal of Bioinformatics and Computational Biology","issn_l":"0219-7200","issn":["0219-7200","1757-6334"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310311754","host_organization_name":"Imperial College Press","host_organization_lineage":["https://openalex.org/P4310311754"],"host_organization_lineage_names":["Imperial College Press"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of Bioinformatics and Computational Biology","raw_type":"journal-article"},"type":"article","indexed_in":["crossref","pubmed"],"open_access":{"is_oa":false,"oa_status":"closed","oa_url":null,"any_repository_has_fulltext":false},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5072507978","display_name":"Rajiv Karbhal","orcid":"https://orcid.org/0000-0002-1927-8366"},"institutions":[{"id":"https://openalex.org/I878213199","display_name":"Savitribai Phule Pune University","ror":"https://ror.org/044g6d731","country_code":"IN","type":"education","lineage":["https://openalex.org/I878213199"]}],"countries":["IN"],"is_corresponding":true,"raw_author_name":"Rajiv Karbhal","raw_affiliation_strings":["Bioinformatics Centre, Savitribai Phule Pune University, Pune 411007, India"],"raw_orcid":"https://orcid.org/0000-0002-1927-8366","affiliations":[{"raw_affiliation_string":"Bioinformatics Centre, Savitribai Phule Pune University, Pune 411007, India","institution_ids":["https://openalex.org/I878213199"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5017628254","display_name":"Sangeeta Sawant","orcid":"https://orcid.org/0000-0002-5098-6387"},"institutions":[{"id":"https://openalex.org/I878213199","display_name":"Savitribai Phule Pune University","ror":"https://ror.org/044g6d731","country_code":"IN","type":"education","lineage":["https://openalex.org/I878213199"]}],"countries":["IN"],"is_corresponding":false,"raw_author_name":"Sangeeta Sawant","raw_affiliation_strings":["Bioinformatics Centre, Savitribai Phule Pune University, Pune 411007, India"],"raw_orcid":"https://orcid.org/0000-0002-5098-6387","affiliations":[{"raw_affiliation_string":"Bioinformatics Centre, Savitribai Phule Pune University, Pune 411007, India","institution_ids":["https://openalex.org/I878213199"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5045189496","display_name":"Urmila Kulkarni\u2010Kale","orcid":"https://orcid.org/0000-0002-1168-2479"},"institutions":[{"id":"https://openalex.org/I2801380234","display_name":"University of South-Eastern Norway","ror":"https://ror.org/05ecg5h20","country_code":"NO","type":"education","lineage":["https://openalex.org/I2801380234"]},{"id":"https://openalex.org/I878213199","display_name":"Savitribai Phule Pune University","ror":"https://ror.org/044g6d731","country_code":"IN","type":"education","lineage":["https://openalex.org/I878213199"]}],"countries":["IN","NO"],"is_corresponding":false,"raw_author_name":"Urmila Kulkarni-Kale","raw_affiliation_strings":["Bioinformatics Centre, Savitribai Phule Pune University, Pune 411007, India","Department of Natural Sciences and Environmental Health, University of Southeastern Norway, Gullbringvegen 36, 3800 B\u00f8, Norway"],"raw_orcid":"https://orcid.org/0000-0002-1168-2479","affiliations":[{"raw_affiliation_string":"Bioinformatics Centre, Savitribai Phule Pune University, Pune 411007, India","institution_ids":["https://openalex.org/I878213199"]},{"raw_affiliation_string":"Department of Natural Sciences and Environmental Health, University of Southeastern Norway, Gullbringvegen 36, 3800 B\u00f8, Norway","institution_ids":["https://openalex.org/I2801380234"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":3,"corresponding_author_ids":["https://openalex.org/A5072507978"],"corresponding_institution_ids":["https://openalex.org/I878213199"],"apc_list":null,"apc_paid":null,"fwci":0.0,"has_fulltext":false,"cited_by_count":0,"citation_normalized_percentile":{"value":0.02844197,"is_in_top_1_percent":false,"is_in_top_10_percent":false},"cited_by_percentile_year":null,"biblio":{"volume":"22","issue":"02","first_page":"2450005","last_page":"2450005"},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T10932","display_name":"Microbial Metabolic Engineering and Bioproduction","score":0.9959999918937683,"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/T10932","display_name":"Microbial Metabolic Engineering and Bioproduction","score":0.9959999918937683,"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/T10519","display_name":"Advanced Proteomics Techniques and Applications","score":0.9901999831199646,"subfield":{"id":"https://openalex.org/subfields/1607","display_name":"Spectroscopy"},"field":{"id":"https://openalex.org/fields/16","display_name":"Chemistry"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},{"id":"https://openalex.org/T10887","display_name":"Bioinformatics and Genomic Networks","score":0.9789999723434448,"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/extraction","display_name":"Extraction (chemistry)","score":0.5164318680763245},{"id":"https://openalex.org/keywords/computer-science","display_name":"Computer science","score":0.4700309932231903},{"id":"https://openalex.org/keywords/computational-biology","display_name":"Computational biology","score":0.4000382423400879},{"id":"https://openalex.org/keywords/data-mining","display_name":"Data mining","score":0.350921094417572},{"id":"https://openalex.org/keywords/artificial-intelligence","display_name":"Artificial intelligence","score":0.32305824756622314},{"id":"https://openalex.org/keywords/information-retrieval","display_name":"Information retrieval","score":0.3209794759750366},{"id":"https://openalex.org/keywords/biology","display_name":"Biology","score":0.3112504482269287},{"id":"https://openalex.org/keywords/chemistry","display_name":"Chemistry","score":0.22099748253822327},{"id":"https://openalex.org/keywords/chromatography","display_name":"Chromatography","score":0.15238186717033386}],"concepts":[{"id":"https://openalex.org/C4725764","wikidata":"https://www.wikidata.org/wiki/Q844704","display_name":"Extraction (chemistry)","level":2,"score":0.5164318680763245},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.4700309932231903},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.4000382423400879},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.350921094417572},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.32305824756622314},{"id":"https://openalex.org/C23123220","wikidata":"https://www.wikidata.org/wiki/Q816826","display_name":"Information retrieval","level":1,"score":0.3209794759750366},{"id":"https://openalex.org/C86803240","wikidata":"https://www.wikidata.org/wiki/Q420","display_name":"Biology","level":0,"score":0.3112504482269287},{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.22099748253822327},{"id":"https://openalex.org/C43617362","wikidata":"https://www.wikidata.org/wiki/Q170050","display_name":"Chromatography","level":1,"score":0.15238186717033386}],"mesh":[{"descriptor_ui":"D004798","descriptor_name":"Enzymes","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":true},{"descriptor_ui":"D004798","descriptor_name":"Enzymes","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":true},{"descriptor_ui":"D004798","descriptor_name":"Enzymes","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":true},{"descriptor_ui":"D004798","descriptor_name":"Enzymes","qualifier_ui":"Q000378","qualifier_name":"metabolism","is_major_topic":true},{"descriptor_ui":"D004798","descriptor_name":"Enzymes","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D004798","descriptor_name":"Enzymes","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D004798","descriptor_name":"Enzymes","qualifier_ui":"Q000737","qualifier_name":"chemistry","is_major_topic":true},{"descriptor_ui":"D004798","descriptor_name":"Enzymes","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":"D014584","descriptor_name":"User-Computer Interface","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D014584","descriptor_name":"User-Computer Interface","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D014584","descriptor_name":"User-Computer Interface","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D014584","descriptor_name":"User-Computer Interface","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D019295","descriptor_name":"Computational Biology","qualifier_ui":"Q000379","qualifier_name":"methods","is_major_topic":false},{"descriptor_ui":"D020407","descriptor_name":"Internet","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020407","descriptor_name":"Internet","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020407","descriptor_name":"Internet","qualifier_ui":null,"qualifier_name":null,"is_major_topic":false},{"descriptor_ui":"D020407","descriptor_name":"Internet","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":true},{"descriptor_ui":"D030562","descriptor_name":"Databases, Protein","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D030562","descriptor_name":"Databases, Protein","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true},{"descriptor_ui":"D030562","descriptor_name":"Databases, Protein","qualifier_ui":null,"qualifier_name":null,"is_major_topic":true}],"locations_count":2,"locations":[{"id":"doi:10.1142/s0219720024500057","is_oa":false,"landing_page_url":"http://dx.doi.org/10.1142/s0219720024500057","pdf_url":null,"source":{"id":"https://openalex.org/S155349577","display_name":"Journal of Bioinformatics and Computational Biology","issn_l":"0219-7200","issn":["0219-7200","1757-6334"],"is_oa":false,"is_in_doaj":false,"is_core":true,"host_organization":"https://openalex.org/P4310311754","host_organization_name":"Imperial College Press","host_organization_lineage":["https://openalex.org/P4310311754"],"host_organization_lineage_names":["Imperial College Press"],"type":"journal"},"license":null,"license_id":null,"version":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Journal of Bioinformatics and Computational Biology","raw_type":"journal-article"},{"id":"pmid:38779780","is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/38779780","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":"Journal of bioinformatics and computational biology","raw_type":null}],"best_oa_location":null,"sustainable_development_goals":[{"id":"https://metadata.un.org/sdg/12","display_name":"Responsible consumption and production","score":0.4300000071525574}],"awards":[],"funders":[],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":40,"referenced_works":["https://openalex.org/W1985512202","https://openalex.org/W1993006803","https://openalex.org/W2074231493","https://openalex.org/W2082593499","https://openalex.org/W2104295259","https://openalex.org/W2107158607","https://openalex.org/W2108723491","https://openalex.org/W2110679449","https://openalex.org/W2111973517","https://openalex.org/W2122559203","https://openalex.org/W2162388472","https://openalex.org/W2218384328","https://openalex.org/W2224812643","https://openalex.org/W2417115050","https://openalex.org/W2546916519","https://openalex.org/W2559588208","https://openalex.org/W2612989432","https://openalex.org/W2804695150","https://openalex.org/W2805241968","https://openalex.org/W2891585877","https://openalex.org/W2892210937","https://openalex.org/W2895689867","https://openalex.org/W2899903294","https://openalex.org/W2900674118","https://openalex.org/W2951793362","https://openalex.org/W2951899941","https://openalex.org/W2977870980","https://openalex.org/W3014856454","https://openalex.org/W3045127574","https://openalex.org/W3048090444","https://openalex.org/W3094217983","https://openalex.org/W3094967361","https://openalex.org/W3095583226","https://openalex.org/W3097145107","https://openalex.org/W3098935468","https://openalex.org/W3112376646","https://openalex.org/W3112600195","https://openalex.org/W3195743182","https://openalex.org/W4225538654","https://openalex.org/W4226250462"],"related_works":["https://openalex.org/W2377297411","https://openalex.org/W3148217948","https://openalex.org/W2375788636","https://openalex.org/W2358561207","https://openalex.org/W2388704129","https://openalex.org/W2392827053","https://openalex.org/W2975617233","https://openalex.org/W3188962172","https://openalex.org/W2377877252","https://openalex.org/W2362914816"],"abstract_inverted_index":{"Enzymes":[0],"catalyze":[1],"diverse":[2],"biochemical":[3],"reactions":[4],"and":[5,11,15,23,37,94,106,128,161,200,212,222],"are":[6,19,24,55,151],"building":[7],"blocks":[8],"of":[9,17,50,52,74,114,130,139,169,190,197],"cellular":[10],"metabolic":[12],"pathways.":[13],"Data":[14,76],"metadata":[16],"enzymes":[18,140],"distributed":[20],"across":[21],"databases":[22,31,93],"archived":[25],"in":[26,41,149],"various":[27],"formats.":[28],"The":[29,143,179],"enzyme":[30,39,92,119,192],"provide":[32,82],"utilities":[33,87,147],"for":[34,60,63,88,112,156,186,208,220],"efficient":[35],"searches":[36],"downloading":[38],"records":[40],"batch":[42],"mode":[43],"but":[44],"do":[45],"not":[46],"support":[47],"organism-specific":[48,83],"extraction":[49,66,86,146],"subsets":[51,196],"data.":[53],"Users":[54],"required":[56],"to":[57,68,81,125,153,165,175],"write":[58],"scripts":[59],"parsing":[61],"entries":[62],"customized":[64,84,144],"data":[65,85,145],"prior":[67],"downstream":[69,209],"analysis.":[70],"Integrated":[71],"Customized":[72],"Extraction":[73],"Enzyme":[75],"(iCEED)":[77],"has":[78],"been":[79],"developed":[80],"seven":[89],"commonly":[90],"used":[91,207,219],"brings":[95],"these":[96],"resources":[97],"under":[98],"an":[99,173],"integrated":[100,180],"portal.":[101],"iCEED":[102,150,203,215],"provides":[103],"dropdown":[104],"menus":[105],"search":[107],"boxes":[108],"using":[109,202],"typehead":[110],"utility":[111,124],"submission":[113],"queries":[115],"as":[116,118],"well":[117],"class-based":[120],"browsing":[121],"utility.":[122],"A":[123],"facilitate":[126],"mapping":[127],"visualization":[129,182],"functionally":[131],"important":[132],"features":[133],"on":[134],"the":[135,191],"three-dimensional":[136],"(3D)":[137],"structures":[138],"is":[141,184],"integrated.":[142],"provided":[148],"expected":[152],"be":[154,205,218],"useful":[155,185],"biochemists,":[157],"biotechnologists,":[158],"computational":[159],"biologists,":[160],"life":[162],"science":[163],"researchers":[164],"build":[166],"curated":[167,201],"datasets":[168],"their":[170],"choice":[171],"through":[172],"easy":[174],"navigate":[176],"web-based":[177],"interface.":[178],"feature":[181],"system":[183],"a":[187],"fine-grained":[188],"understanding":[189],"structure-function":[193],"relationship.":[194],"Desired":[195],"data,":[198],"extracted":[199],"can":[204,216],"subsequently":[206],"processing,":[210],"analyses,":[211],"knowledge":[213],"discovery.":[214],"also":[217],"training":[221],"teaching":[223],"purposes.":[224]},"counts_by_year":[],"updated_date":"2026-05-21T06:26:12.895304","created_date":"2025-10-10T00:00:00"}
