{"id":"https://openalex.org/W7203580295","doi":"https://doi.org/10.64898/2026.10.18.759859","title":"The accessible human surfaceome","display_name":"The accessible human surfaceome","publication_year":2026,"publication_date":"2026-10-19","ids":{"openalex":"https://openalex.org/W7203580295","doi":"https://doi.org/10.64898/2026.10.18.759859"},"language":"en","primary_location":{"id":"doi:10.64898/2026.10.18.759859","doi":"https://doi.org/10.64898/2026.10.18.759859","is_oa":true,"landing_page_url":"https://doi.org/10.64898/2026.10.18.759859","pdf_url":null,"source":{"id":"https://openalex.org/S4306402567","display_name":"bioRxiv (Cold Spring Harbor Laboratory)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":"https://openalex.org/I2750212522","host_organization_name":"Cold Spring Harbor Laboratory","host_organization_lineage":["https://openalex.org/I2750212522"],"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":"bioRxiv","raw_type":"posted-content"},"volume":null,"type":"preprint","is_traditional":true,"indexed_in":["crossref","datacite"],"open_access":{"is_oa":true,"oa_status":"green","oa_url":"https://doi.org/10.64898/2026.10.18.759859","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5102319305","display_name":"Rebecca Carlson","orcid":"https://orcid.org/0000-0002-5423-9717","observed_orcids":["https://orcid.org/0000-0002-5423-9717"]},"institutions":[],"countries":[],"is_corresponding":true,"raw_author_name":"Rebecca J. Carlson","raw_affiliation_strings":["Deliverome Bio;"],"raw_orcid":"https://orcid.org/0000-0002-5423-9717","affiliations":[{"raw_affiliation_string":"Deliverome Bio;","institution_ids":[]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5040105991","display_name":"Louis Robert Hollingsworth","orcid":"https://orcid.org/0000-0002-4130-3580","observed_orcids":["https://orcid.org/0000-0002-4130-3580"]},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"L. Robert Hollingsworth","raw_affiliation_strings":["Deliverome Bio;"],"raw_orcid":"https://orcid.org/0000-0002-4130-3580","affiliations":[{"raw_affiliation_string":"Deliverome Bio;","institution_ids":[]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5039181413","display_name":"Michael J. Smallegan","orcid":"https://orcid.org/0000-0002-5919-6736","observed_orcids":["https://orcid.org/0000-0002-5919-6736"]},"institutions":[],"countries":[],"is_corresponding":false,"raw_author_name":"Michael J. Smallegan","raw_affiliation_strings":["Coral Bio"],"raw_orcid":"https://orcid.org/0000-0002-5919-6736","affiliations":[{"raw_affiliation_string":"Coral Bio","institution_ids":[]}]}],"institutions":[],"countries_distinct_count":0,"institutions_distinct_count":0,"corresponding_author_ids":["https://openalex.org/A5102319305"],"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/T11710","display_name":"Biomedical Text Mining and Ontologies","score":0.7782999873161316,"subfield":{"id":"https://openalex.org/subfields/2718","display_name":"Health Informatics"},"field":{"id":"https://openalex.org/fields/27","display_name":"Medicine"},"domain":{"id":"https://openalex.org/domains/4","display_name":"Health Sciences"}},"topics":[{"id":"https://openalex.org/T11710","display_name":"Biomedical Text Mining and Ontologies","score":0.7782999873161316,"subfield":{"id":"https://openalex.org/subfields/2718","display_name":"Health Informatics"},"field":{"id":"https://openalex.org/fields/27","display_name":"Medicine"},"domain":{"id":"https://openalex.org/domains/4","display_name":"Health Sciences"}},{"id":"https://openalex.org/T12254","display_name":"Machine Learning in Bioinformatics","score":0.13850000500679016,"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/T10887","display_name":"Bioinformatics and Genomic Networks","score":0.02630000002682209,"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/plasma-membrane-proteome","display_name":"plasma membrane proteome","score":0.8389999866485596},{"id":"https://openalex.org/keywords/literature-curation","display_name":"literature curation","score":0.6589999794960022},{"id":"https://openalex.org/keywords/therapeutic-target","display_name":"therapeutic target","score":0.5690000057220459},{"id":"https://openalex.org/keywords/protein-localization","display_name":"protein localization","score":0.503000020980835}],"concepts":[{"id":"https://openalex.org/C2780416260","wikidata":"https://www.wikidata.org/wiki/Q2063","display_name":"JSON","level":2,"score":0.6507999897003174},{"id":"https://openalex.org/C2780551164","wikidata":"https://www.wikidata.org/wiki/Q2306599","display_name":"Column (typography)","level":3,"score":0.6320000290870667},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.6060000061988831},{"id":"https://openalex.org/C38721330","wikidata":"https://www.wikidata.org/wiki/Q80056","display_name":"Sonnet","level":3,"score":0.5501000285148621},{"id":"https://openalex.org/C135598885","wikidata":"https://www.wikidata.org/wiki/Q1366302","display_name":"Row","level":2,"score":0.3993000090122223},{"id":"https://openalex.org/C23123220","wikidata":"https://www.wikidata.org/wiki/Q816826","display_name":"Information retrieval","level":1,"score":0.39660000801086426},{"id":"https://openalex.org/C140146324","wikidata":"https://www.wikidata.org/wiki/Q1144319","display_name":"Predicate (mathematical logic)","level":2,"score":0.39500001072883606},{"id":"https://openalex.org/C2779913896","wikidata":"https://www.wikidata.org/wiki/Q7063001","display_name":"Notice","level":2,"score":0.32499998807907104},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.3021000027656555},{"id":"https://openalex.org/C136886441","wikidata":"https://www.wikidata.org/wiki/Q926129","display_name":"Normalization (sociology)","level":2,"score":0.2851000130176544},{"id":"https://openalex.org/C183003079","wikidata":"https://www.wikidata.org/wiki/Q1000371","display_name":"Personalization","level":2,"score":0.2644999921321869},{"id":"https://openalex.org/C2781067378","wikidata":"https://www.wikidata.org/wiki/Q17027399","display_name":"Interpretability","level":2,"score":0.2624000012874603},{"id":"https://openalex.org/C34736171","wikidata":"https://www.wikidata.org/wiki/Q918333","display_name":"Preprocessor","level":2,"score":0.2621000111103058},{"id":"https://openalex.org/C13743948","wikidata":"https://www.wikidata.org/wiki/Q45842","display_name":"Web crawler","level":2,"score":0.26089999079704285},{"id":"https://openalex.org/C2777212361","wikidata":"https://www.wikidata.org/wiki/Q5127848","display_name":"Class (philosophy)","level":2,"score":0.2587999999523163},{"id":"https://openalex.org/C124101348","wikidata":"https://www.wikidata.org/wiki/Q172491","display_name":"Data mining","level":1,"score":0.257099986076355},{"id":"https://openalex.org/C204321447","wikidata":"https://www.wikidata.org/wiki/Q30642","display_name":"Natural language processing","level":1,"score":0.25679999589920044},{"id":"https://openalex.org/C185798385","wikidata":"https://www.wikidata.org/wiki/Q1161707","display_name":"Benchmark (surveying)","level":2,"score":0.25600001215934753}],"mesh":[],"locations_count":4,"locations":[{"id":"doi:10.64898/2026.10.18.759859","doi":"https://doi.org/10.64898/2026.10.18.759859","is_oa":true,"landing_page_url":"https://doi.org/10.64898/2026.10.18.759859","pdf_url":null,"source":{"id":"https://openalex.org/S4306402567","display_name":"bioRxiv (Cold Spring Harbor Laboratory)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":"https://openalex.org/I2750212522","host_organization_name":"Cold Spring Harbor Laboratory","host_organization_lineage":["https://openalex.org/I2750212522"],"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":"bioRxiv","raw_type":"posted-content"},{"id":"doi:10.5281/zenodo.20805383","doi":"https://doi.org/10.5281/zenodo.20805383","is_oa":true,"landing_page_url":"https://doi.org/10.5281/zenodo.20805383","pdf_url":null,"source":{"id":"https://openalex.org/S4306400562","display_name":"Zenodo (CERN European Organization for Nuclear Research)","issn_l":null,"issn":null,"is_oa":true,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":"https://openalex.org/I67311998","host_organization_name":"European Organization for Nuclear Research","host_organization_lineage":["https://openalex.org/I67311998"],"host_organization_lineage_names":[],"type":"repository"},"license":"public-domain","license_id":"https://openalex.org/licenses/public-domain","version":null,"is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"Dataset"},{"id":"doi:10.5281/zenodo.20805384","doi":"https://doi.org/10.5281/zenodo.20805384","is_oa":true,"landing_page_url":"https://doi.org/10.5281/zenodo.20805384","pdf_url":null,"source":{"id":"https://openalex.org/S4306400562","display_name":"Zenodo (CERN European Organization for Nuclear Research)","issn_l":null,"issn":null,"is_oa":true,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":"https://openalex.org/I67311998","host_organization_name":"European Organization for Nuclear Research","host_organization_lineage":["https://openalex.org/I67311998"],"host_organization_lineage_names":[],"type":"repository"},"license":"public-domain","license_id":"https://openalex.org/licenses/public-domain","version":null,"is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"Dataset"},{"id":"doi:10.5281/zenodo.23445521","doi":"https://doi.org/10.5281/zenodo.23445521","is_oa":true,"landing_page_url":"https://doi.org/10.5281/zenodo.23445521","pdf_url":null,"source":{"id":"https://openalex.org/S4306400562","display_name":"Zenodo (CERN European Organization for Nuclear Research)","issn_l":null,"issn":null,"is_oa":true,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":"https://openalex.org/I67311998","host_organization_name":"European Organization for Nuclear Research","host_organization_lineage":["https://openalex.org/I67311998"],"host_organization_lineage_names":[],"type":"repository"},"license":"public-domain","license_id":"https://openalex.org/licenses/public-domain","version":null,"is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"Dataset"}],"best_oa_location":{"id":"doi:10.64898/2026.10.18.759859","doi":"https://doi.org/10.64898/2026.10.18.759859","is_oa":true,"landing_page_url":"https://doi.org/10.64898/2026.10.18.759859","pdf_url":null,"source":{"id":"https://openalex.org/S4306402567","display_name":"bioRxiv (Cold Spring Harbor Laboratory)","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":"https://openalex.org/I2750212522","host_organization_name":"Cold Spring Harbor Laboratory","host_organization_lineage":["https://openalex.org/I2750212522"],"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":"bioRxiv","raw_type":"posted-content"},"sustainable_development_goals":[{"score":0.5683000087738037,"display_name":"Good health and well-being","id":"https://metadata.un.org/sdg/3"}],"study_designs":[],"awards":[],"funders":[],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":0,"referenced_works":[],"related_works":["https://openalex.org/W2904567776","https://openalex.org/W2898873576","https://openalex.org/W4383501139","https://openalex.org/W1989762591","https://openalex.org/W3014027811","https://openalex.org/W3135173565","https://openalex.org/W4404529887","https://openalex.org/W2037942444","https://openalex.org/W7125900310","https://openalex.org/W2581250028"],"abstract_inverted_index":{"Proteins":[0],"associated":[1],"with":[2,159],"the":[3,7,13,45,55,77,134,194,202],"extracellular":[4],"face":[5],"of":[6,57,93,125,138],"plasma":[8,47],"membrane":[9,48],"(\"surface":[10],"proteins\"":[11],"or":[12,161],"\"surfaceome\")":[14],"are":[15],"important":[16],"therapeutic":[17,66],"targets":[18],"because":[19],"they":[20],"can":[21,210,227],"direct":[22],"therapeutics":[23],"to":[24,75,193,198,243],"specific":[25],"cell":[26],"types":[27],"and":[28,35,50,115,130,157,176,182,197],"deliver":[29],"them":[30],"into":[31],"cells.":[32],"However,":[33],"experimental":[34],"computational":[36],"databases":[37,100,114,231],"disagree":[38],"substantially":[39],"on":[40,54,96,147],"which":[41,97],"proteins":[42,60,95,120,156],"make":[43],"up":[44],"human":[46,79],"proteome,":[49],"none":[51],"focus":[52],"specifically":[53],"set":[56],"accessible":[58,78],"surface":[59,108,119,132,140,155,163],"that":[61,220,232],"would":[62],"be":[63,211],"useful":[64],"for":[65],"applications.":[67],"Here,":[68],"we":[69,86],"used":[70],"an":[71,214],"agentic":[72],"LLM":[73,104],"pipeline":[74,135,145],"curate":[76],"surfaceome":[80],"from":[81,201],"literature.":[82,245],"To":[83],"assess":[84],"performance,":[85],"built":[87],"SurfaceBench,":[88],"a":[89],"manually":[90],"curated":[91],"benchmark":[92],"147":[94],"five":[98],"reference":[99],"frequently":[101],"disagree.":[102],"Our":[103],"triage":[105],"agent":[106,241],"classified":[107],"status":[109],"more":[110],"accurately":[111],"than":[112],"existing":[113,186],"recovered":[116,136],"1,108":[117],"candidate":[118],"not":[121],"present":[122],"in":[123,213],"any":[124],"them.":[126],"On":[127],"held-out":[128],"clinical":[129],"viral-entry":[131],"targets,":[133],"98\u2013100%":[137],"established":[139],"antigens.":[141],"A":[142],"literature-anchored":[143],"deep-dive":[144],"run":[146],"over":[148,223],"5,000":[149],"candidates":[150],"then":[151],"returned":[152],"1,783":[153],"canonical":[154],"1,252":[158],"weaker":[160],"context-dependent":[162],"evidence.":[164],"Each":[165],"queryable":[166],"record":[167],"contains":[168],"24":[169],"LLM-based":[170],"annotation":[171],"fields\u2014including":[172],"confidence,":[173],"primary":[174],"localization,":[175],"expression":[177],"breadth\u2014and":[178],"seven":[179],"deterministic":[180],"structural":[181],"topological":[183],"features.":[184],"Unlike":[185],"databases,":[187],"our":[188],"records":[189,209],"trace":[190],"every":[191],"claim":[192],"agent's":[195],"reasoning":[196,222],"exact":[199],"quotes":[200],"full-text":[203,244],"literature":[204],"it":[205],"could":[206],"access.":[207],"All":[208],"browsed":[212],"open-source":[215],"viewer.":[216],"These":[217],"results":[218],"show":[219],"LLMs":[221],"unstructured":[224],"scientific":[225],"text":[226],"build":[228],"updatable,":[229],"bespoke":[230],"outperform":[233],"expert-curated":[234],"resources,":[235],"although":[236],"performance":[237],"remains":[238],"limited":[239],"by":[240],"access":[242]},"counts_by_year":[],"updated_date":"2026-11-09T13:22:03.289127","created_date":"2026-08-17T00:00:00"}