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

[11] Single-nucleus cross-tissue molecular reference maps toward understanding disease gene function [J].

Eraslan, Gokcen ;

Drokhlyansky, Eugene ;

Anand, Shankara ;

Fiskin, Evgenij ;

Subramanian, Ayshwarya ;

Slyper, Michal ;

Wang, Jiali ;

Van Wittenberghe, Nicholas ;

Rouhana, John M. ;

Waldman, Julia ;

Ashenberg, Orr ;

Lek, Monkol ;

Dionne, Danielle ;

Win, Thet Su ;

Cuoco, Michael S. ;

Kuksenko, Olena ;

Tsankov, Alexander M. ;

Branton, Philip A. ;

Marshall, Jamie L. ;

Greka, Anna ;

Getz, Gad ;

Segre, Ayellet, V ;

Aguet, Francois ;

Rozenblatt-Rosen, Orit ;

Ardlie, Kristin G. ;

Regev, Aviv .

SCIENCE, 2022, 376 (6594) :712-+

[12] SemOpenAlex: The Scientific Landscape in 26 Billion RDF Triples [J].

Faerber, Michael ;

Lamprecht, David ;

Krause, Johan ;

Aung, Linn ;

Haase, Peter .

SEMANTIC WEB, ISWC 2023, PT II, 2023, 14266 :94-112

[13] Science of science [J].

Fortunato, Santo ;

Bergstrom, Carl T. ;

Boerner, Katy ;

Evans, James A. ;

Helbing, Dirk ;

Milojevic, Stasa ;

Petersen, Alexander M. ;

Radicchi, Filippo ;

Sinatra, Roberta ;

Uzzi, Brian ;

Vespignani, Alessandro ;

Waltman, Ludo ;

Wang, Dashun ;

Barabasi, Albert-Laszlo .

SCIENCE, 2018, 359 (6379)

[14] Guided construction of single cell reference for human and mouse lung [J].

Guo, Minzhe ;

Morley, Michael P. ;

Jiang, Cheng ;

Wu, Yixin ;

Li, Guangyuan ;

Du, Yina ;

Zhao, Shuyang ;

Wagner, Andrew ;

Cakar, Adnan Cihan ;

Kouril, Michal A. ;

Jin, Kang ;

Gaddis, Nathan C. ;

Kitzmiller, Joseph A. M. ;

Stewart, Kathleen ;

Basil, Maria C. ;

Lin, Susan M. A. ;

Ying, Yun ;

Babu, Apoorva P. ;

Wikenheiser-Brokamp, Kathryn A. ;

Mun, Kyu Shik N. ;

Naren, Anjaparavanda P. S. ;

Clair, Geremy S. ;

Adkins, Joshua N. J. ;

Pryhuber, Gloria S. L. ;

Misra, Ravi S. ;

Aronow, Bruce J. ;

Tickle, Timothy L. E. ;

Salomonis, Nathan A. ;

Sun, Xin ;

Morrisey, Edward E. ;

Whitsett, Jeffrey A. ;

Xu, Yan .

NATURE COMMUNICATIONS, 2023, 14 (01)

[15] Crossref: The sustainable source of community-owned scholarly metadata [J].

Hendricks, Ginny ;

Tkaczyk, Dominika ;

Lin, Jennifer ;

Feeney, Patricia .

QUANTITATIVE SCIENCE STUDIES, 2020, 1 (01) :414-427

[16] Specimen, biological structure, and spatial ontologies in support of a Human Reference Atlas [J].

Herr, Bruce W., II ;

Hardi, Josef ;

Quardokus, Ellen M. ;

Bueckle, Andreas ;

Chen, Lu ;

Wang, Fusheng ;

Caron, Anita R. ;

Osumi-Sutherland, David ;

Musen, Mark A. ;

Borner, Katy .

SCIENTIFIC DATA, 2023, 10 (01)

[17] Systematic integration of biomedical knowledge prioritizes drugs for repurposing [J].

Himmelstein, Daniel Scott ;

Lizee, Antoine ;

Hessler, Christine ;

Brueggeman, Leo ;

Chen, Sabrina L. ;

Hadley, Dexter ;

Green, Ari ;

Khankhanian, Pouya ;

Baranzini, Sergio E. .

ELIFE, 2017, 6

[18] Advances and prospects for the Human BioMolecular Atlas Program (HuBMAP) [J].

Jain, Sanjay ;

Pei, Liming ;

Spraggins, Jeffrey M. ;

Angelo, Michael ;

Carson, James P. ;

Gehlenborg, Nils ;

Ginty, Fiona ;

Goncalves, Joana P. ;

Hagood, James S. ;

Hickey, John W. ;

Kelleher, Neil L. ;

Laurent, Louise C. ;

Lin, Shin ;

Lin, Yiing ;

Liu, Huiping ;

Naba, Alexandra ;

Nakayasu, Ernesto S. ;

Qian, Wei-Jun ;

Radtke, Andrea ;

Robson, Paul ;

Stockwell, Brent R. ;

Van de Plas, Raf ;

Vlachos, Ioannis S. ;

Zhou, Mowei ;

Boerner, Katy ;

Snyder, Michael P. ;

Ahn, Kyung Jin ;

Allen, Jamie ;

Anderson, David M. ;

Anderton, Christopher R. ;

Curcio, Christine ;

Angelin, Alessia ;

Arvanitis, Constadina ;

Atta, Lyla ;

Awosika-Olumo, Demi ;

Bahmani, Amir ;

Bai, Huajun ;

Balderrama, Karol ;

Balzano, Leandro ;

Bandyopadhyay, Gautam ;

Bandyopadhyay, Shovik ;

Bar-Joseph, Ziv ;

Barnhart, Kurt ;

Barwinska, Daria ;

Becich, Michael ;

Becker, Laren ;

Becker, Winston ;

Bedi, Kenneth ;

Bendall, Sean ;

Benninger, Kathy .

NATURE CELL BIOLOGY, 2023, 25 (08) :1089-1100

[19] How are exclusively data journals indexed in major scholarly databases? An examination of four databases [J].

Jiao, Chenyue ;

Li, Kai ;

Fang, Zhichao .

SCIENTIFIC DATA, 2023, 10 (01)

[20] The BRAIN Initiative: developing technology to catalyse neuroscience discovery [J].

Jorgenson, Lyric A. ;

Newsome, William T. ;

Anderson, David J. ;

Bargmann, Cornelia I. ;

Brown, Emery N. ;

Deisseroth, Karl ;

Donoghue, John P. ;

Hudson, Kathy L. ;

Ling, Geoffrey S. F. ;

MacLeish, Peter R. ;

Marder, Eve ;

Normann, Richard A. ;

Sanes, Joshua R. ;

Schnitzer, Mark J. ;

Sejnowski, Terrence J. ;

Tank, David W. ;

Tsien, Roger Y. ;

Ugurbil, Kamil ;

Wingfield, John C. .

PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES, 2015, 370 (1668) :8-19

← 1 2 3 4 5 →