{"id":"https://openalex.org/W7129224998","doi":"https://doi.org/10.21203/rs.3.rs-8774770/v1","title":"OmniCellTOSG: The First Cell Text-Omic Signaling Graphs Dataset for Graph Language Foundation Modeling","display_name":"OmniCellTOSG: The First Cell Text-Omic Signaling Graphs Dataset for Graph Language Foundation Modeling","publication_year":2026,"publication_date":"2026-02-17","ids":{"openalex":"https://openalex.org/W7129224998","doi":"https://doi.org/10.21203/rs.3.rs-8774770/v1","pmid":"https://pubmed.ncbi.nlm.nih.gov/41756454","pmcid":"https://www.ncbi.nlm.nih.gov/pmc/articles/12934919"},"language":"en","primary_location":{"id":"doi:10.21203/rs.3.rs-8774770/v1","doi":"https://doi.org/10.21203/rs.3.rs-8774770/v1","is_oa":true,"landing_page_url":"https://doi.org/10.21203/rs.3.rs-8774770/v1","pdf_url":null,"source":{"id":"https://openalex.org/S4306525896","display_name":"Research Square","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"acceptedVersion","is_accepted":true,"is_published":false,"raw_source_name":"Research Square","raw_type":"posted-content"},"volume":null,"type":"preprint","indexed_in":["arxiv","crossref","datacite","pubmed"],"open_access":{"is_oa":true,"oa_status":"green","oa_url":"https://doi.org/10.21203/rs.3.rs-8774770/v1","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5077409027","display_name":"Fuhai Li","orcid":"https://orcid.org/0000-0002-3773-146X","observed_orcids":["https://orcid.org/0000-0002-3773-146X"]},"institutions":[{"id":"https://openalex.org/I204465549","display_name":"Washington University in St. Louis","ror":"https://ror.org/01yc7t268","country_code":"US","type":"education","lineage":["https://openalex.org/I204465549"]}],"countries":["US"],"is_corresponding":true,"raw_author_name":"Fuhai Li","raw_affiliation_strings":["Washington University in St Louis"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Washington University in St Louis","institution_ids":["https://openalex.org/I204465549"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5079056336","display_name":"Heming Zhang","orcid":"https://orcid.org/0000-0002-2025-9090","observed_orcids":["https://orcid.org/0000-0002-2025-9090"]},"institutions":[{"id":"https://openalex.org/I204465549","display_name":"Washington University in St. Louis","ror":"https://ror.org/01yc7t268","country_code":"US","type":"education","lineage":["https://openalex.org/I204465549"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Heming Zhang","raw_affiliation_strings":["Washington University in St Louis"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Washington University in St Louis","institution_ids":["https://openalex.org/I204465549"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5137996727","display_name":"Tim Xu","orcid":null,"observed_orcids":[]},"institutions":[{"id":"https://openalex.org/I204465549","display_name":"Washington University in St. Louis","ror":"https://ror.org/01yc7t268","country_code":"US","type":"education","lineage":["https://openalex.org/I204465549"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Tim Xu","raw_affiliation_strings":["Washington University in St Louis"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Washington University in St Louis","institution_ids":["https://openalex.org/I204465549"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5101357382","display_name":"Dekang Cao","orcid":null,"observed_orcids":[]},"institutions":[{"id":"https://openalex.org/I204465549","display_name":"Washington University in St. Louis","ror":"https://ror.org/01yc7t268","country_code":"US","type":"education","lineage":["https://openalex.org/I204465549"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Dekang Cao","raw_affiliation_strings":["Washington University in St Louis"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Washington University in St Louis","institution_ids":["https://openalex.org/I204465549"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5078196450","display_name":"Shu Ying Liang","orcid":"https://orcid.org/0000-0002-7018-4672","observed_orcids":["https://orcid.org/0000-0002-7018-4672"]},"institutions":[{"id":"https://openalex.org/I204465549","display_name":"Washington University in St. Louis","ror":"https://ror.org/01yc7t268","country_code":"US","type":"education","lineage":["https://openalex.org/I204465549"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Shunning Liang","raw_affiliation_strings":["Washington University in St Louis"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Washington University in St Louis","institution_ids":["https://openalex.org/I204465549"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5126220668","display_name":"Guntaas Shergill","orcid":"https://orcid.org/0009-0002-2949-9223","observed_orcids":["https://orcid.org/0009-0002-2949-9223"]},"institutions":[{"id":"https://openalex.org/I204465549","display_name":"Washington University in St. Louis","ror":"https://ror.org/01yc7t268","country_code":"US","type":"education","lineage":["https://openalex.org/I204465549"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Guntaas Shergill","raw_affiliation_strings":["Washington University in St Louis"],"raw_orcid":"https://orcid.org/0009-0002-2949-9223","affiliations":[{"raw_affiliation_string":"Washington University in St Louis","institution_ids":["https://openalex.org/I204465549"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5104988116","display_name":"Nicholas Hadas","orcid":null,"observed_orcids":[]},"institutions":[{"id":"https://openalex.org/I204465549","display_name":"Washington University in St. Louis","ror":"https://ror.org/01yc7t268","country_code":"US","type":"education","lineage":["https://openalex.org/I204465549"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Nicholas Hadas","raw_affiliation_strings":["Washington University in St Louis"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Washington University in St Louis","institution_ids":["https://openalex.org/I204465549"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5117290849","display_name":"Lars E. Schimmelpfennig","orcid":"https://orcid.org/0009-0009-0585-2062","observed_orcids":["https://orcid.org/0009-0009-0585-2062"]},"institutions":[{"id":"https://openalex.org/I204465549","display_name":"Washington University in St. Louis","ror":"https://ror.org/01yc7t268","country_code":"US","type":"education","lineage":["https://openalex.org/I204465549"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Lars Schimmelpfennig","raw_affiliation_strings":["Washington University in St Louis"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Washington University in St Louis","institution_ids":["https://openalex.org/I204465549"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5095746379","display_name":"Levi Kaster","orcid":"https://orcid.org/0009-0002-3773-801X","observed_orcids":["https://orcid.org/0009-0002-3773-801X"]},"institutions":[{"id":"https://openalex.org/I204465549","display_name":"Washington University in St. Louis","ror":"https://ror.org/01yc7t268","country_code":"US","type":"education","lineage":["https://openalex.org/I204465549"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Levi Kaster","raw_affiliation_strings":["Washington University in St Louis"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Washington University in St Louis","institution_ids":["https://openalex.org/I204465549"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5101445950","display_name":"Di Huang","orcid":"https://orcid.org/0009-0004-0573-190X","observed_orcids":["https://orcid.org/0009-0004-0573-190X"]},"institutions":[{"id":"https://openalex.org/I204465549","display_name":"Washington University in St. Louis","ror":"https://ror.org/01yc7t268","country_code":"US","type":"education","lineage":["https://openalex.org/I204465549"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Di Huang","raw_affiliation_strings":["Washington University in St Louis"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Washington University in St Louis","institution_ids":["https://openalex.org/I204465549"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5126242685","display_name":"Guangfu Li","orcid":null,"observed_orcids":[]},"institutions":[{"id":"https://openalex.org/I140172145","display_name":"University of Connecticut","ror":"https://ror.org/02der9h97","country_code":"US","type":"education","lineage":["https://openalex.org/I140172145"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Guangfu Li","raw_affiliation_strings":["University of Connecticut"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"University of Connecticut","institution_ids":["https://openalex.org/I140172145"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5126193537","display_name":"S. Goedegebuure","orcid":null,"observed_orcids":[]},"institutions":[{"id":"https://openalex.org/I204465549","display_name":"Washington University in St. Louis","ror":"https://ror.org/01yc7t268","country_code":"US","type":"education","lineage":["https://openalex.org/I204465549"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"S. Goedegebuure","raw_affiliation_strings":["Washington University in St.Louis"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Washington University in St.Louis","institution_ids":["https://openalex.org/I204465549"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5066901504","display_name":"David G. DeNardo","orcid":"https://orcid.org/0000-0002-3655-5783","observed_orcids":["https://orcid.org/0000-0002-3655-5783"]},"institutions":[{"id":"https://openalex.org/I204465549","display_name":"Washington University in St. Louis","ror":"https://ror.org/01yc7t268","country_code":"US","type":"education","lineage":["https://openalex.org/I204465549"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"David DeNardo","raw_affiliation_strings":["Washington University in St. Louis"],"raw_orcid":"https://orcid.org/0000-0002-3655-5783","affiliations":[{"raw_affiliation_string":"Washington University in St. Louis","institution_ids":["https://openalex.org/I204465549"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5126190553","display_name":"Li Ding","orcid":"https://orcid.org/0000-0003-1517-2975","observed_orcids":["https://orcid.org/0000-0003-1517-2975"]},"institutions":[{"id":"https://openalex.org/I204465549","display_name":"Washington University in St. Louis","ror":"https://ror.org/01yc7t268","country_code":"US","type":"education","lineage":["https://openalex.org/I204465549"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Li Ding","raw_affiliation_strings":["Washington University in St. Louis"],"raw_orcid":"https://orcid.org/0000-0003-1517-2975","affiliations":[{"raw_affiliation_string":"Washington University in St. Louis","institution_ids":["https://openalex.org/I204465549"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5081302342","display_name":"Ryan Courtney Fields","orcid":"https://orcid.org/0000-0001-6176-8943","observed_orcids":["https://orcid.org/0000-0001-6176-8943"]},"institutions":[{"id":"https://openalex.org/I204465549","display_name":"Washington University in St. Louis","ror":"https://ror.org/01yc7t268","country_code":"US","type":"education","lineage":["https://openalex.org/I204465549"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Ryan Fields","raw_affiliation_strings":["Washington University in St Louis"],"raw_orcid":"https://orcid.org/0000-0001-6176-8943","affiliations":[{"raw_affiliation_string":"Washington University in St Louis","institution_ids":["https://openalex.org/I204465549"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5126215835","display_name":"J Philip Miller","orcid":null,"observed_orcids":[]},"institutions":[{"id":"https://openalex.org/I204465549","display_name":"Washington University in St. Louis","ror":"https://ror.org/01yc7t268","country_code":"US","type":"education","lineage":["https://openalex.org/I204465549"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"J Philip Miller","raw_affiliation_strings":["Washington University in St Louis"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Washington University in St Louis","institution_ids":["https://openalex.org/I204465549"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5042095567","display_name":"Pirooz Eghtesady","orcid":"https://orcid.org/0000-0001-7161-8391","observed_orcids":["https://orcid.org/0000-0001-7161-8391"]},"institutions":[{"id":"https://openalex.org/I204465549","display_name":"Washington University in St. Louis","ror":"https://ror.org/01yc7t268","country_code":"US","type":"education","lineage":["https://openalex.org/I204465549"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Pirooz Eghtesady","raw_affiliation_strings":["Washington University in St Louis"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Washington University in St Louis","institution_ids":["https://openalex.org/I204465549"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5040490170","display_name":"Carlos Cruchaga","orcid":"https://orcid.org/0000-0002-0276-2899","observed_orcids":["https://orcid.org/0000-0002-0276-2899","https://orcid.org/0000-0002-5261-689X"]},"institutions":[{"id":"https://openalex.org/I204465549","display_name":"Washington University in St. Louis","ror":"https://ror.org/01yc7t268","country_code":"US","type":"education","lineage":["https://openalex.org/I204465549"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Carlos Cruchaga","raw_affiliation_strings":["Washington University School of Medicine"],"raw_orcid":"https://orcid.org/0000-0002-0276-2899","affiliations":[{"raw_affiliation_string":"Washington University School of Medicine","institution_ids":["https://openalex.org/I204465549"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5068633977","display_name":"William Buchser","orcid":"https://orcid.org/0000-0002-6675-6359","observed_orcids":["https://orcid.org/0000-0002-6675-6359"]},"institutions":[{"id":"https://openalex.org/I204465549","display_name":"Washington University in St. Louis","ror":"https://ror.org/01yc7t268","country_code":"US","type":"education","lineage":["https://openalex.org/I204465549"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"William Buchser","raw_affiliation_strings":["Washington University in St. Louis"],"raw_orcid":"https://orcid.org/0000-0002-6675-6359","affiliations":[{"raw_affiliation_string":"Washington University in St. Louis","institution_ids":["https://openalex.org/I204465549"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5070668450","display_name":"Jonathan D. Cooper","orcid":"https://orcid.org/0000-0003-1339-4750","observed_orcids":["https://orcid.org/0000-0003-1339-4750"]},"institutions":[{"id":"https://openalex.org/I204465549","display_name":"Washington University in St. Louis","ror":"https://ror.org/01yc7t268","country_code":"US","type":"education","lineage":["https://openalex.org/I204465549"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Jonathan Cooper","raw_affiliation_strings":["Washington University in St. Louis"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Washington University in St. Louis","institution_ids":["https://openalex.org/I204465549"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5081495214","display_name":"Marco Sardiello","orcid":"https://orcid.org/0000-0001-6484-0250","observed_orcids":["https://orcid.org/0000-0001-6484-0250"]},"institutions":[{"id":"https://openalex.org/I204465549","display_name":"Washington University in St. Louis","ror":"https://ror.org/01yc7t268","country_code":"US","type":"education","lineage":["https://openalex.org/I204465549"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Marco Sardiello","raw_affiliation_strings":["Washington University in St. Louis"],"raw_orcid":"https://orcid.org/0000-0001-6484-0250","affiliations":[{"raw_affiliation_string":"Washington University in St. Louis","institution_ids":["https://openalex.org/I204465549"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5112081854","display_name":"PATRICIA DICKSON","orcid":"https://orcid.org/0000-0003-3467-8488","observed_orcids":["https://orcid.org/0000-0003-3467-8488"]},"institutions":[{"id":"https://openalex.org/I204465549","display_name":"Washington University in St. Louis","ror":"https://ror.org/01yc7t268","country_code":"US","type":"education","lineage":["https://openalex.org/I204465549"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Patricia Dickson","raw_affiliation_strings":["Washington University in St. Louis"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Washington University in St. Louis","institution_ids":["https://openalex.org/I204465549"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5107503552","display_name":"Yixin Chen","orcid":null,"observed_orcids":[]},"institutions":[{"id":"https://openalex.org/I204465549","display_name":"Washington University in St. Louis","ror":"https://ror.org/01yc7t268","country_code":"US","type":"education","lineage":["https://openalex.org/I204465549"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Yixin Chen","raw_affiliation_strings":["Washington University in St. Louis"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Washington University in St. Louis","institution_ids":["https://openalex.org/I204465549"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5004832167","display_name":"Michael A. Province","orcid":"https://orcid.org/0000-0001-6102-774X","observed_orcids":["https://orcid.org/0000-0001-6102-774X"]},"institutions":[{"id":"https://openalex.org/I204465549","display_name":"Washington University in St. Louis","ror":"https://ror.org/01yc7t268","country_code":"US","type":"education","lineage":["https://openalex.org/I204465549"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Michael Province","raw_affiliation_strings":["Washington University"],"raw_orcid":"https://orcid.org/0000-0001-6102-774X","affiliations":[{"raw_affiliation_string":"Washington University","institution_ids":["https://openalex.org/I204465549"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5035864539","display_name":"Philip P. R. Payne","orcid":"https://orcid.org/0000-0002-9532-2998","observed_orcids":["https://orcid.org/0000-0002-9532-2998"]},"institutions":[{"id":"https://openalex.org/I204465549","display_name":"Washington University in St. Louis","ror":"https://ror.org/01yc7t268","country_code":"US","type":"education","lineage":["https://openalex.org/I204465549"]}],"countries":["US"],"is_corresponding":false,"raw_author_name":"Philip Payne","raw_affiliation_strings":["Washington University in St.Louis"],"raw_orcid":null,"affiliations":[{"raw_affiliation_string":"Washington University in St.Louis","institution_ids":["https://openalex.org/I204465549"]}]}],"institutions":[],"countries_distinct_count":1,"institutions_distinct_count":2,"corresponding_author_ids":["https://openalex.org/A5077409027"],"corresponding_institution_ids":["https://openalex.org/I204465549"],"apc_list":null,"apc_paid":null,"fwci":null,"has_fulltext":false,"cited_by_count":3,"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/T10887","display_name":"Bioinformatics and Genomic Networks","score":0.7782999873161316,"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":0.7782999873161316,"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/T11289","display_name":"Single-cell and spatial transcriptomics","score":0.21449999511241913,"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/T10621","display_name":"Gene Regulatory Network Analysis","score":0.002099999925121665,"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/single-cell-rna-sequencing","display_name":"single-cell RNA sequencing","score":0.7879999876022339},{"id":"https://openalex.org/keywords/single-nucleus-rna-sequencing","display_name":"single-nucleus RNA sequencing","score":0.9860000014305115},{"id":"https://openalex.org/keywords/biomedical-knowledge-integration","display_name":"biomedical knowledge integration","score":0.656000018119812},{"id":"https://openalex.org/keywords/signaling-pathways","display_name":"signaling pathways","score":0.609000027179718}],"concepts":[{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.5985000133514404},{"id":"https://openalex.org/C132525143","wikidata":"https://www.wikidata.org/wiki/Q141488","display_name":"Graph","level":2,"score":0.5110999941825867},{"id":"https://openalex.org/C152662350","wikidata":"https://www.wikidata.org/wiki/Q815297","display_name":"Systems biology","level":2,"score":0.5037000179290771},{"id":"https://openalex.org/C2780801425","wikidata":"https://www.wikidata.org/wiki/Q5164392","display_name":"Construct (python library)","level":2,"score":0.49380001425743103},{"id":"https://openalex.org/C70721500","wikidata":"https://www.wikidata.org/wiki/Q177005","display_name":"Computational biology","level":1,"score":0.43849998712539673},{"id":"https://openalex.org/C67339327","wikidata":"https://www.wikidata.org/wiki/Q1502576","display_name":"Gene regulatory network","level":4,"score":0.3790000081062317},{"id":"https://openalex.org/C2522767166","wikidata":"https://www.wikidata.org/wiki/Q2374463","display_name":"Data science","level":1,"score":0.37630000710487366},{"id":"https://openalex.org/C28225019","wikidata":"https://www.wikidata.org/wiki/Q4915005","display_name":"Biological network","level":2,"score":0.3718999922275543},{"id":"https://openalex.org/C111696304","wikidata":"https://www.wikidata.org/wiki/Q2303697","display_name":"Sorting","level":2,"score":0.34689998626708984},{"id":"https://openalex.org/C154945302","wikidata":"https://www.wikidata.org/wiki/Q11660","display_name":"Artificial intelligence","level":1,"score":0.33340001106262207},{"id":"https://openalex.org/C206345919","wikidata":"https://www.wikidata.org/wiki/Q20380951","display_name":"Resource (disambiguation)","level":2,"score":0.3255000114440918},{"id":"https://openalex.org/C72634772","wikidata":"https://www.wikidata.org/wiki/Q386824","display_name":"Data integration","level":2,"score":0.3212999999523163},{"id":"https://openalex.org/C88230418","wikidata":"https://www.wikidata.org/wiki/Q131476","display_name":"Graph theory","level":2,"score":0.31369999051094055},{"id":"https://openalex.org/C2780966255","wikidata":"https://www.wikidata.org/wiki/Q5474306","display_name":"Foundation (evidence)","level":2,"score":0.30230000615119934},{"id":"https://openalex.org/C189206191","wikidata":"https://www.wikidata.org/wiki/Q222046","display_name":"Genomics","level":4,"score":0.3018999993801117},{"id":"https://openalex.org/C201797286","wikidata":"https://www.wikidata.org/wiki/Q4914986","display_name":"Biological data","level":2,"score":0.29660001397132874},{"id":"https://openalex.org/C2987255567","wikidata":"https://www.wikidata.org/wiki/Q33002955","display_name":"Knowledge graph","level":2,"score":0.2872999906539917},{"id":"https://openalex.org/C32946077","wikidata":"https://www.wikidata.org/wiki/Q618079","display_name":"Network analysis","level":2,"score":0.2856000065803528},{"id":"https://openalex.org/C15152581","wikidata":"https://www.wikidata.org/wiki/Q7833966","display_name":"Transduction (biophysics)","level":2,"score":0.2667999863624573},{"id":"https://openalex.org/C176225458","wikidata":"https://www.wikidata.org/wiki/Q595971","display_name":"Graph database","level":3,"score":0.2639000117778778},{"id":"https://openalex.org/C162317418","wikidata":"https://www.wikidata.org/wiki/Q252857","display_name":"Transcriptome","level":4,"score":0.25839999318122864},{"id":"https://openalex.org/C60644358","wikidata":"https://www.wikidata.org/wiki/Q128570","display_name":"Bioinformatics","level":1,"score":0.25290000438690186},{"id":"https://openalex.org/C137753397","wikidata":"https://www.wikidata.org/wiki/Q2434424","display_name":"Network science","level":3,"score":0.25029999017715454}],"mesh":[],"locations_count":5,"locations":[{"id":"doi:10.21203/rs.3.rs-8774770/v1","doi":"https://doi.org/10.21203/rs.3.rs-8774770/v1","is_oa":true,"landing_page_url":"https://doi.org/10.21203/rs.3.rs-8774770/v1","pdf_url":null,"source":{"id":"https://openalex.org/S4306525896","display_name":"Research Square","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"acceptedVersion","is_accepted":true,"is_published":false,"raw_source_name":"Research Square","raw_type":"posted-content"},{"id":"pmid:41756454","doi":null,"is_oa":false,"landing_page_url":"https://pubmed.ncbi.nlm.nih.gov/41756454","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,"listed_in":[],"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":"Research square","raw_type":"Journal Article"},{"id":"pmh:oai:pubmedcentral.nih.gov:12934919","doi":null,"is_oa":true,"landing_page_url":"https://pmc.ncbi.nlm.nih.gov/articles/PMC12934919/","pdf_url":null,"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,"listed_in":[],"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":"publishedVersion","is_accepted":true,"is_published":true,"raw_source_name":"Res Sq","raw_type":"Text"},{"id":"pmh:oai:arXiv.org:2504.02148","doi":null,"is_oa":true,"landing_page_url":"http://arxiv.org/abs/2504.02148","pdf_url":"https://arxiv.org/pdf/2504.02148","source":{"id":"https://openalex.org/S4306400194","display_name":"arXiv (Cornell University)","issn_l":"2331-8422","issn":["2331-8422"],"is_oa":true,"is_in_doaj":false,"is_core":false,"listed_in":[],"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":null,"license_id":null,"version":"submittedVersion","is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"text"},{"id":"doi:10.48550/arxiv.2504.02148","doi":"https://doi.org/10.48550/arxiv.2504.02148","is_oa":true,"landing_page_url":"https://doi.org/10.48550/arxiv.2504.02148","pdf_url":null,"source":{"id":"https://openalex.org/S4306400194","display_name":"arXiv (Cornell University)","issn_l":"2331-8422","issn":["2331-8422"],"is_oa":true,"is_in_doaj":false,"is_core":false,"listed_in":[],"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":null,"license_id":null,"version":null,"is_accepted":false,"is_published":false,"raw_source_name":null,"raw_type":"Preprint"}],"best_oa_location":{"id":"doi:10.21203/rs.3.rs-8774770/v1","doi":"https://doi.org/10.21203/rs.3.rs-8774770/v1","is_oa":true,"landing_page_url":"https://doi.org/10.21203/rs.3.rs-8774770/v1","pdf_url":null,"source":{"id":"https://openalex.org/S4306525896","display_name":"Research Square","issn_l":null,"issn":null,"is_oa":false,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"acceptedVersion","is_accepted":true,"is_published":false,"raw_source_name":"Research Square","raw_type":"posted-content"},"sustainable_development_goals":[],"study_designs":[],"awards":[{"id":"https://openalex.org/G1871403720","display_name":"AI models of multi-omic data integration for ming longevity core signaling pathways","funder_award_id":"1r21ag078799-01a1","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G2084029995","display_name":"Modeling and targeting tumor-immune signaling interactions in tumor microenvironment","funder_award_id":"5r01lm013902-02","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G4742389823","display_name":"Systems-Level Approach to Neuronopathic Lysosomal Storage Disorders","funder_award_id":"5rm1ns132962-02","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"},{"id":"https://openalex.org/G6499737016","display_name":"Combine Genomics and Symptoms Data Driven Models to Discover Synergistic Combinatory Therapies for Alzheimer's Disease","funder_award_id":"R56AG065352","funder_id":"https://openalex.org/F4320337337","funder_display_name":"National Institute on Aging"},{"id":"https://openalex.org/G9000912901","display_name":"AI models of multi-omic data integration for ming longevity core signaling pathways","funder_award_id":"4r33ag078799-02","funder_id":"https://openalex.org/F4320332161","funder_display_name":"National Institutes of Health"}],"funders":[{"id":"https://openalex.org/F4320332161","display_name":"National Institutes of Health","ror":"https://ror.org/01cwqze88"},{"id":"https://openalex.org/F4320337337","display_name":"National Institute on Aging","ror":"https://ror.org/049v75w11"}],"has_content":{"grobid_xml":false,"pdf":false},"content_urls":null,"referenced_works_count":0,"referenced_works":[],"related_works":["https://openalex.org/W7165555890","https://openalex.org/W4401351748","https://openalex.org/W4416199280","https://openalex.org/W4327675690","https://openalex.org/W7160548690","https://openalex.org/W7171786840","https://openalex.org/W4225278475","https://openalex.org/W4414837140","https://openalex.org/W4412163730","https://openalex.org/W4408537402"],"abstract_inverted_index":{"Abstract":[0],"With":[1],"the":[2,64],"rapid":[3],"growth":[4],"of":[5,48],"large-scale":[6,93],"single-cell":[7,106],"omic":[8,10,31,80,128,140],"datasets,":[9],"foundation":[11],"models":[12],"(FMs)":[13],"have":[14],"emerged":[15],"as":[16,42],"powerful":[17],"tools":[18],"for":[19,58],"advancing":[20],"research":[21],"in":[22],"life":[23],"sciences":[24],"and":[25,52,82,107,113,129,142,149],"precision":[26],"medicine.":[27],"However,":[28],"most":[29],"existing":[30,139],"FMs":[32],"rely":[33],"primarily":[34],"on":[35],"numerical":[36],"transcriptomic":[37],"data":[38,71],"by":[39],"sorting":[40],"genes":[41],"sequences,":[43],"while":[44],"lacking":[45],"explicit":[46],"integration":[47],"biomedical":[49,76],"prior":[50],"knowledge":[51],"signaling":[53,83,130,150],"interactions":[54],"that":[55,73],"are":[56],"critical":[57],"scientific":[59],"discovery.":[60],"Here,":[61],"we":[62,89],"introduce":[63],"Text-Omic":[65],"Signaling":[66],"Graph":[67],"(TOSG),":[68],"a":[69,92,119],"novel":[70],"structure":[72],"unifies":[74],"human-interpretable":[75],"textual":[77],"knowledge,":[78],"quantitative":[79],"data,":[81],"network":[84,131],"information.":[85],"Using":[86],"this":[87],"framework,":[88],"construct":[90],"OmniCellTOSG,":[91],"resource":[94],"comprising":[95],"approximately":[96],"half":[97],"million":[98,105],"meta-cell":[99],"TOSGs":[100],"derived":[101],"from":[102],"around":[103],"80":[104],"single-nucleus":[108],"RNA-seq":[109],"profiles":[110],"across":[111],"organs":[112],"diseases.":[114],"We":[115],"further":[116],"develop":[117],"CellTOSG-FM,":[118],"multimodal":[120],"graph":[121],"language":[122],"FM,":[123],"to":[124],"jointly":[125],"analyze":[126],"textual,":[127],"context.":[132],"Across":[133],"diverse":[134],"downstream":[135],"tasks,":[136],"CellTOSG-FM":[137],"outperforms":[138],"FMs,":[141],"provides":[143],"interpretable":[144],"insights":[145],"into":[146],"disease-associated":[147],"targets":[148],"pathways.":[151]},"counts_by_year":[{"year":2026,"cited_by_count":2},{"year":2025,"cited_by_count":1}],"updated_date":"2026-10-31T12:09:11.096373","created_date":"2026-02-18T00:00:00"}
