Publication, funding, and experimental data in support of Human Reference Atlas construction and usage

被引：3

作者：

Kong, Yongxin ^{[1
,2
]}

Borner, Katy ^{[1
]}

机构：

[1] Indiana Univ, Luddy Sch Informat Comp & Engn, Dept Intelligent Syst Engn, Bloomington, IN 47408 USA

[2] Sun Yat Sen Univ, Sch Informat Management, Guangzhou 510006, Peoples R China

来源：

SCIENTIFIC DATA | 2024年 / 11卷 / 01期

关键词：

D O I：

10.1038/s41597-024-03416-8

中图分类号：

O [数理科学和化学]; P [天文学、地球科学]; Q [生物科学]; N [自然科学总论];

学科分类号：

07 ; 0710 ; 09 ;

摘要：

Experts from 18 consortia are collaborating on the Human Reference Atlas (HRA) which aims to map the 37 trillion cells in the healthy human body. Information relevant for HRA construction and usage is held by experts, published in scholarly papers, and captured in experimental data. However, these data sources use different metadata schemas and cannot be cross-searched efficiently. This paper documents the compilation of a dataset, named HRAlit, that links the 136 HRA v1.4 digital objects (31 organs with 4,279 anatomical structures, 1,210 cell types, 2,089 biomarkers) to 583,117 experts; 7,103,180 publications; 896,680 funded projects, and 1,816 experimental datasets. The resulting HRAlit has 22 tables with 20,939,937 records including 6 junction tables with 13,170,651 relationships. The HRAlit can be mined to identify leading experts, major papers, funding trends, or alignment with existing ontologies in support of systematic HRA construction and usage.

引用

页数：10

共 41 条

[1]

[Anonymous], 2023, Release v1.4 DOI Landing Pages

[2] pubmed2ensembl: A Resource for Mining the Biological Literature on Genes [J].

Baran, Joachim ;

Gerner, Martin ;

Haeussler, Maximilian ;

Nenadic, Goran ;

Bergman, Casey M. .

PLOS ONE, 2011, 6 (09)

[3] A biomedical open knowledge network harnesses the power of AI to understand deep human biology [J].

Baranzini, Sergio E. ;

Borner, Katy ;

Morris, John ;

Nelson, Charlotte A. ;

Soman, Karthik ;

Schleimer, Erica ;

Keiser, Michael ;

Musen, Mark ;

Pearce, Roger ;

Reza, Tahsin ;

Smith, Brett ;

Herr, Bruce W., II ;

Oskotsky, Boris ;

Rizk-Jackson, Angela ;

Rankin, Katherine P. ;

Sanders, Stephan J. ;

Bove, Riley ;

Rose, Peter W. ;

Israni, Sharat ;

Huang, Sui .

AI MAGAZINE, 2022, 43 (01) :46-58

[4] A collection of read depth profiles at structural variant breakpoints [J].

Bezdvornykh, Igor ;

Cherkasov, Nikolay ;

Kanapin, Alexander ;

Samsonova, Anastasia .

SCIENTIFIC DATA, 2023, 10 (01)

[5] Tissue registration and exploration user interfaces in support of a human reference atlas [J].

Borner, Katy ;

Bueckle, Andreas ;

Herr, Bruce W. ;

Cross, Leonard E. ;

Quardokus, Ellen M. ;

Record, Elizabeth G. ;

Ju, Yingnan ;

Silverstein, Jonathan C. ;

Browne, Kristen M. ;

Jain, Sanjay ;

Wasserfall, Clive H. ;

Jorgensen, Marda L. ;

Spraggins, Jeffrey M. ;

Patterson, N. Heath ;

Weber, Griffin M. .

COMMUNICATIONS BIOLOGY, 2022, 5 (01)

[6] Anatomical structures, cell types and biomarkers of the Human Reference Atlas [J].

Borner, Katy ;

Teichmann, Sarah A. ;

Quardokus, Ellen M. ;

Gee, James C. ;

Browne, Kristen ;

Osumi-Sutherland, David ;

Herr, Bruce W., II ;

Bueckle, Andreas ;

Paul, Hrishikesh ;

Haniffa, Muzlifah ;

Jardine, Laura ;

Bernard, Amy ;

Ding, Song-Lin ;

Miller, Jeremy A. ;

Lin, Shin ;

Halushka, Marc K. ;

Boppana, Avinash ;

Longacre, Teri A. ;

Hickey, John ;

Lin, Yiing ;

Valerius, M. Todd ;

He, Yongqun ;

Pryhuber, Gloria ;

Sun, Xin ;

Jorgensen, Marda ;

Radtke, Andrea J. ;

Wasserfall, Clive ;

Ginty, Fiona ;

Ho, Jonhan ;

Sunshine, Joel ;

Beuschel, Rebecca T. ;

Brusko, Maigan ;

Lee, Sujin ;

Malhotra, Rajeev ;

Jain, Sanjay ;

Weber, Griffin .

NATURE CELL BIOLOGY, 2021, 23 (11) :1117-1128

[7] Growth rates of modern science: a latent piecewise growth curve approach to model publication numbers from established and new literature databases [J].

Bornmann, Lutz ;

Haunschild, Robin ;

Mutz, Rudiger .

HUMANITIES & SOCIAL SCIENCES COMMUNICATIONS, 2021, 8 (01)

[8]

Chan Zuckerberg Initiative, 2022, Chan Zuckerberg CELLxGENE Discover

[9] The Personal Genome Project-UK, an open access resource of human multi-omics data [J].

Chervova, Olga ;

Conde, Lucia ;

Guerra-Assuncao, Jose Afonso ;

Moghul, Ismail ;

Webster, Amy P. ;

Berner, Alison ;

Cadieux, Elizabeth Larose ;

Tian, Yuan ;

Voloshin, Vitaly ;

Jesus, Tiago F. ;

Hamoudi, Rifat ;

Herrero, Javier ;

Beck, Stephan .

SCIENTIFIC DATA, 2019, 6 (1)

[10] A multimodal and integrated approach to interrogate human kidney biopsies with rigor and reproducibility: guidelines from the Kidney Precision Medicine Project [J].

El-Achkar, Tarek M. ;

Eadon, Michael T. ;

Menon, Rajasree ;

Lake, Blue B. ;

Sigdel, Tara K. ;

Alexandrov, Theodore ;

Parikh, Samir ;

Zhang, Guanshi ;

Dobi, Dejan ;

Dunn, Kenneth W. ;

Otto, Edgar A. ;

Anderton, Christopher R. ;

Carson, Jonas M. ;

Luo, Jinghui ;

Park, Chris ;

Hamidi, Habib ;

Zhou, Jian ;

Hoover, Paul ;

Schroeder, Andrew ;

Joanes, Marianinha ;

Azeloglu, Evren U. ;

Sealfon, Rachel ;

Winfree, Seth ;

Steck, Becky ;

He, Yongqun ;

D'Agati, Vivette ;

Iyengar, Ravi ;

Troyanskaya, Olga G. ;

Barisoni, Laura ;

Gaut, Joseph ;

Zhang, Kun ;

Laszik, Zoltan ;

Rovin, Brad H. ;

Dagher, Pierre C. ;

Sharma, Kumar ;

Sarwal, Minnie M. ;

Hodgin, Jeffrey B. ;

Alpers, Charles E. ;

Kretzler, Matthias ;

Jain, Sanjay .

PHYSIOLOGICAL GENOMICS, 2021, 53 (01) :1-11

← 1 2 3 4 5 →