{"id":"https://openalex.org/W7161028602","doi":"https://doi.org/10.48550/arxiv.2605.11221","title":"Beyond Manual Curation: Augmenting Targeted Protein Degradation Databases via Agentic Literature Extraction Workflows","display_name":"Beyond Manual Curation: Augmenting Targeted Protein Degradation Databases via Agentic Literature Extraction Workflows","publication_year":2026,"publication_date":"2026-05-11","ids":{"openalex":"https://openalex.org/W7161028602","doi":"https://doi.org/10.48550/arxiv.2605.11221"},"language":null,"primary_location":{"id":"doi:10.48550/arxiv.2605.11221","is_oa":true,"landing_page_url":"https://doi.org/10.48550/arxiv.2605.11221","pdf_url":null,"source":{"id":"https://openalex.org/S4306400194","display_name":"arXiv (Cornell University)","issn_l":null,"issn":null,"is_oa":true,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I205783295","host_organization_name":"Cornell University","host_organization_lineage":["https://openalex.org/I205783295"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":null,"is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"article"},"type":"preprint","indexed_in":["datacite"],"open_access":{"is_oa":true,"oa_status":"green","oa_url":"https://doi.org/10.48550/arxiv.2605.11221","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5136039305","display_name":"Yaochen Rao","orcid":null},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Rao, Yaochen","raw_affiliation_strings":[],"raw_orcid":null,"affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5088074505","display_name":"Farzaneh Jalalypour","orcid":"https://orcid.org/0000-0001-5092-1914"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Jalalypour, Farzaneh","raw_affiliation_strings":[],"raw_orcid":null,"affiliations":[]},{"author_position":"middle","author":{"id":"https://openalex.org/A5065129881","display_name":"N. M. Anoop Krishnan","orcid":"https://orcid.org/0000-0003-1500-4947"},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Krishnan, N. M. Anoop","raw_affiliation_strings":[],"raw_orcid":null,"affiliations":[]},{"author_position":"last","author":{"id":"https://openalex.org/A5136032213","display_name":"Roc\u00edo Mercado","orcid":null},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Mercado, Roc\u00edo","raw_affiliation_strings":[],"raw_orcid":null,"affiliations":[]}],"institutions":[],"countries_distinct_count":0,"institutions_distinct_count":4,"corresponding_author_ids":[],"corresponding_institution_ids":[],"apc_list":null,"apc_paid":null,"fwci":null,"has_fulltext":false,"cited_by_count":0,"citation_normalized_percentile":null,"cited_by_percentile_year":null,"biblio":{"volume":null,"issue":null,"first_page":null,"last_page":null},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T12534","display_name":"Protein Degradation and Inhibitors","score":0.6434000134468079,"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/T12534","display_name":"Protein Degradation and Inhibitors","score":0.6434000134468079,"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/T10211","display_name":"Computational Drug Discovery Methods","score":0.04540000110864639,"subfield":{"id":"https://openalex.org/subfields/1703","display_name":"Computational Theory and Mathematics"},"field":{"id":"https://openalex.org/fields/17","display_name":"Computer Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},{"id":"https://openalex.org/T11440","display_name":"Click Chemistry and Applications","score":0.033900000154972076,"subfield":{"id":"https://openalex.org/subfields/1605","display_name":"Organic Chemistry"},"field":{"id":"https://openalex.org/fields/16","display_name":"Chemistry"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/workflow","display_name":"Workflow","score":0.8011000156402588},{"id":"https://openalex.org/keywords/data-curation","display_name":"Data curation","score":0.7242000102996826},{"id":"https://openalex.org/keywords/context","display_name":"Context (archaeology)","score":0.6794999837875366},{"id":"https://openalex.org/keywords/bottleneck","display_name":"Bottleneck","score":0.5843999981880188},{"id":"https://openalex.org/keywords/task","display_name":"Task (project management)","score":0.4862000048160553},{"id":"https://openalex.org/keywords/identifier","display_name":"Identifier","score":0.4465999901294708},{"id":"https://openalex.org/keywords/information-extraction","display_name":"Information extraction","score":0.42289999127388},{"id":"https://openalex.org/keywords/data-extraction","display_name":"Data extraction","score":0.39989998936653137}],"concepts":[{"id":"https://openalex.org/C177212765","wikidata":"https://www.wikidata.org/wiki/Q627335","display_name":"Workflow","level":2,"score":0.8011000156402588},{"id":"https://openalex.org/C91632574","wikidata":"https://www.wikidata.org/wiki/Q15088675","display_name":"Data curation","level":2,"score":0.7242000102996826},{"id":"https://openalex.org/C2779343474","wikidata":"https://www.wikidata.org/wiki/Q3109175","display_name":"Context (archaeology)","level":2,"score":0.6794999837875366},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6650000214576721},{"id":"https://openalex.org/C77088390","wikidata":"https://www.wikidata.org/wiki/Q8513","display_name":"Database","level":1,"score":0.6151999831199646},{"id":"https://openalex.org/C2780513914","wikidata":"https://www.wikidata.org/wiki/Q18210350","display_name":"Bottleneck","level":2,"score":0.5843999981880188},{"id":"https://openalex.org/C2780451532","wikidata":"https://www.wikidata.org/wiki/Q759676","display_name":"Task (project management)","level":2,"score":0.4862000048160553},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.45239999890327454},{"id":"https://openalex.org/C154504017","wikidata":"https://www.wikidata.org/wiki/Q853614","display_name":"Identifier","level":2,"score":0.4465999901294708},{"id":"https://openalex.org/C195807954","wikidata":"https://www.wikidata.org/wiki/Q1662562","display_name":"Information extraction","level":2,"score":0.42289999127388},{"id":"https://openalex.org/C23123220","wikidata":"https://www.wikidata.org/wiki/Q816826","display_name":"Information retrieval","level":1,"score":0.4169999957084656},{"id":"https://openalex.org/C2777466982","wikidata":"https://www.wikidata.org/wiki/Q5227287","display_name":"Data extraction","level":3,"score":0.39989998936653137},{"id":"https://openalex.org/C66782513","wikidata":"https://www.wikidata.org/wiki/Q864601","display_name":"Biomedicine","level":2,"score":0.3767000138759613},{"id":"https://openalex.org/C2779679103","wikidata":"https://www.wikidata.org/wiki/Q5251805","display_name":"Degradation (telecommunications)","level":2,"score":0.3280999958515167},{"id":"https://openalex.org/C547195049","wikidata":"https://www.wikidata.org/wiki/Q1725664","display_name":"Terminology","level":2,"score":0.3028999865055084},{"id":"https://openalex.org/C120567893","wikidata":"https://www.wikidata.org/wiki/Q1582085","display_name":"Knowledge extraction","level":2,"score":0.30250000953674316},{"id":"https://openalex.org/C72634772","wikidata":"https://www.wikidata.org/wiki/Q386824","display_name":"Data integration","level":2,"score":0.2987000048160553},{"id":"https://openalex.org/C111219384","wikidata":"https://www.wikidata.org/wiki/Q6954384","display_name":"NIST","level":2,"score":0.2985000014305115},{"id":"https://openalex.org/C47487241","wikidata":"https://www.wikidata.org/wiki/Q5227230","display_name":"Data access","level":2,"score":0.29510000348091125},{"id":"https://openalex.org/C43521106","wikidata":"https://www.wikidata.org/wiki/Q2165493","display_name":"Pipeline (software)","level":2,"score":0.2919999957084656},{"id":"https://openalex.org/C3102742","wikidata":"https://www.wikidata.org/wiki/Q6031177","display_name":"Information repository","level":3,"score":0.28700000047683716},{"id":"https://openalex.org/C2779135771","wikidata":"https://www.wikidata.org/wiki/Q403574","display_name":"Named-entity recognition","level":3,"score":0.2833000123500824},{"id":"https://openalex.org/C2522767166","wikidata":"https://www.wikidata.org/wiki/Q2374463","display_name":"Data science","level":1,"score":0.2768000066280365},{"id":"https://openalex.org/C79158427","wikidata":"https://www.wikidata.org/wiki/Q485396","display_name":"Analytics","level":2,"score":0.26080000400543213},{"id":"https://openalex.org/C153604712","wikidata":"https://www.wikidata.org/wiki/Q7310755","display_name":"Relationship extraction","level":3,"score":0.25360000133514404}],"mesh":[],"locations_count":1,"locations":[{"id":"doi:10.48550/arxiv.2605.11221","is_oa":true,"landing_page_url":"https://doi.org/10.48550/arxiv.2605.11221","pdf_url":null,"source":{"id":"https://openalex.org/S4306400194","display_name":"arXiv (Cornell University)","issn_l":null,"issn":null,"is_oa":true,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I205783295","host_organization_name":"Cornell University","host_organization_lineage":["https://openalex.org/I205783295"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":null,"is_accepted":false,"is_published":null,"raw_source_name":null,"raw_type":"article"}],"best_oa_location":{"id":"doi:10.48550/arxiv.2605.11221","is_oa":true,"landing_page_url":"https://doi.org/10.48550/arxiv.2605.11221","pdf_url":null,"source":{"id":"https://openalex.org/S4306400194","display_name":"arXiv (Cornell University)","issn_l":null,"issn":null,"is_oa":true,"is_in_doaj":false,"is_core":false,"host_organization":"https://openalex.org/I205783295","host_organization_name":"Cornell University","host_organization_lineage":["https://openalex.org/I205783295"],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":null,"is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"article"},"sustainable_development_goals":[],"awards":[],"funders":[],"has_content":{"pdf":false,"grobid_xml":false},"content_urls":null,"referenced_works_count":0,"referenced_works":[],"related_works":[],"abstract_inverted_index":{"Predictive":[0],"models":[1],"in":[2,10,24],"biomedicine":[3],"depend":[4],"on":[5],"structured":[6],"assay":[7,31,40,59],"data":[8,222],"locked":[9],"the":[11,84,141,210],"text,":[12],"tables,":[13,48],"and":[14,42,49,55,75,81,101,118,148,168,173,179,196,204,215,224],"supplements":[15],"of":[16,181],"primary":[17],"publications.":[18],"This":[19],"bottleneck":[20],"is":[21],"especially":[22],"acute":[23],"targeted":[25],"protein":[26],"degradation":[27,37,206],"(TPD),":[28],"where":[29],"each":[30],"record":[32],"must":[33],"combine":[34],"compound":[35,53],"identity,":[36],"target,":[38],"recruiter,":[39],"context,":[41],"endpoint":[43],"values":[44],"reported":[45],"across":[46],"sections,":[47],"supplementary":[50],"files.":[51],"Inconsistent":[52],"identifiers":[54],"incomplete":[56],"or":[57],"implicit":[58],"context":[60,86],"further":[61],"demand":[62],"domain-specific":[63,98],"logic":[64],"that":[65],"generic":[66],"LLM":[67,105,113],"pipelines":[68],"do":[69],"not":[70],"provide.":[71],"Existing":[72],"molecular":[73,138,166],"glue":[74,139,167],"PROTAC":[76,169],"databases":[77,170],"are":[78],"manually":[79],"curated":[80],"often":[82],"lack":[83],"experimental":[85],"required":[87],"for":[88,200,220],"downstream":[89],"modeling.":[90,207],"We":[91,208],"formulate":[92],"TPD":[93,221],"database":[94],"extraction":[95,128],"as":[96,186,218],"a":[97,109],"curation":[99,223,227],"task":[100],"present":[102],"an":[103],"expert-in-the-loop":[104],"workflow,":[106,211],"evaluated":[107],"through":[108],"triangular":[110],"comparison":[111,203],"among":[112],"predictions,":[114],"standardized":[115],"baseline":[116],"records,":[117,175],"expert-annotated":[119],"ground":[120],"truth.":[121],"A":[122],"lightweight":[123],"cross-validated":[124],"prompt-refinement":[125],"module":[126],"adapts":[127],"instructions":[129],"from":[130],"scarce":[131],"expert":[132,189],"annotations.":[133],"With":[134],"only":[135],"seven":[136],"annotated":[137],"publications,":[140],"workflow":[142,192],"achieved":[143],"record-level":[144,157],"$F_1":[145,158],"=":[146],"0.98$":[147],"transferred":[149],"to":[150],"PROTACs":[151],"by":[152,171],"terminology":[153],"substitution":[154],"alone,":[155],"maintaining":[156],">":[159],"0.93$.":[160],"Applied":[161],"at":[162],"scale,":[163],"it":[164],"expanded":[165],"81%":[172],"92%":[174,178],"respectively,":[176],"with":[177],"82.5%":[180],"newly":[182],"recovered":[183,194],"records":[184],"validated":[185],"correct":[187],"upon":[188],"review.":[190],"The":[191],"also":[193],"kinetic":[195],"assay-context":[197],"information":[198],"essential":[199],"cross-study":[201],"potency":[202],"condition-aware":[205],"release":[209],"prompts,":[212],"evaluation":[213],"code,":[214],"extracted":[216],"datasets":[217],"resources":[219],"AI-assisted":[225],"scientific":[226],"more":[228],"broadly.":[229]},"counts_by_year":[],"updated_date":"2026-06-11T09:08:48.828518","created_date":"2026-05-14T00:00:00"}