TY - JOUR
T1 - Tissue registration and exploration user interfaces in support of a human reference atlas
AU - Börner, Katy
AU - Bueckle, Andreas
AU - Herr, Bruce W.
AU - Cross, Leonard E.
AU - Quardokus, Ellen M.
AU - Record, Elizabeth G.
AU - Ju, Yingnan
AU - Silverstein, Jonathan C.
AU - Browne, Kristen M.
AU - Jain, Sanjay
AU - Wasserfall, Clive H.
AU - Jorgensen, Marda L.
AU - Spraggins, Jeffrey M.
AU - Patterson, N. Heath
AU - Weber, Griffin M.
N1 - Funding Information:
We appreciate close collaboration with fellow HuBMAP components TMC-Vanderbilt, TMC-UCSD, TMC-Florida, and the IEC, as well as with the NIH’s National Institute of Allergy and Infectious Diseases (NIAID). Bill Shirey (University of Pittsburgh) supported the users of our interfaces during the data ingest into the HuBMAP ecosystem. Kristin Ardlie (Broad Institute) facilitated data interoperability between the GTEx project and HuBMAP. Seth Winfree (University of Nebraska Medical Center) and Peter Hanna (University of California, Los Angeles) used the CCF RUI to register tissue blocks for KPMP and SPARC, respectively. Michela Noseda (Imperial College London) assisted us with spatially registering HCA extraction sites and landmarks for the heart. David Osumi-Sutherland (European Molecular Biology Laboratory) and Alexander Diehl (University of Buffalo) provided expert input on extracting a non-developmental, healthy human subset of Uberon and Cell Ontology. Zorina S. Galis and Tyler Best (NIH) expertly commented on an early draft of this paper. Todd Theriault copy-edited the paper. Tracey Theriault assisted with the figures. This research has been funded by the National Institutes of Health under Human Biomolecular Atlas Program (HuBMAP) awards OT2OD026671 [K.B., A.B., B.W.H., L.E.C., E.M.Q., E.G.R., Y.J., G.M.W.], OT2OD026675 [J.C.S.], U54AI142766 [C.H.W., M.L.J.], U54DK120058 [J.M.S., N.H.P.], and U54HL145608 [S.J.]; by the Cellular Senescence Network (SenNet) Consortium Organization and Data Coordinating Center (CODCC) award 1U24CA268108-01 [K.B., A.B., B.W.H., E.M.Q., E.G.R., Y.J., J.C.S.]; by the National Institute of Diabetes and Digestive and Kidney Diseases (NIDDK) Kidney Precision Medicine Project grant U2CDK114886 [K.B., E.M.Q., Y.J.]; by the Common Fund Data Ecosystem (CFDE) award OTA 20-005 OT2 OD030545 [K.B., Y.J.]; and the National Institute of Allergy and Infectious Diseases (NIAID), Department of Health and Human Services under BCBB Support Services Contract HHSN316201300006W/HHSN27200002 [K.M.B.]. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the paper. The views and conclusions contained in this document are those of the authors and should not be interpreted as representing the official policies, either expressed or implied, of the NIH.
Funding Information:
We appreciate close collaboration with fellow HuBMAP components TMC-Vanderbilt, TMC-UCSD, TMC-Florida, and the IEC, as well as with the NIH’s National Institute of Allergy and Infectious Diseases (NIAID). Bill Shirey (University of Pittsburgh) supported the users of our interfaces during the data ingest into the HuBMAP ecosystem. Kristin Ardlie (Broad Institute) facilitated data interoperability between the GTEx project and HuBMAP. Seth Winfree (University of Nebraska Medical Center) and Peter Hanna (University of California, Los Angeles) used the CCF RUI to register tissue blocks for KPMP and SPARC, respectively. Michela Noseda (Imperial College London) assisted us with spatially registering HCA extraction sites and landmarks for the heart. David Osumi-Sutherland (European Molecular Biology Laboratory) and Alexander Diehl (University of Buffalo) provided expert input on extracting a non-developmental, healthy human subset of Uberon and Cell Ontology. Zorina S. Galis and Tyler Best (NIH) expertly commented on an early draft of this paper. Todd Theriault copy-edited the paper. Tracey Theriault assisted with the figures. This research has been funded by the National Institutes of Health under Human Biomolecular Atlas Program (HuBMAP) awards OT2OD026671 [K.B., A.B., B.W.H., L.E.C., E.M.Q., E.G.R., Y.J., G.M.W.], OT2OD026675 [J.C.S.], U54AI142766 [C.H.W., M.L.J.], U54DK120058 [J.M.S., N.H.P.], and U54HL145608 [S.J.]; by the Cellular Senescence Network (SenNet) Consortium Organization and Data Coordinating Center (CODCC) award 1U24CA268108-01 [K.B., A.B., B.W.H., E.M.Q., E.G.R., Y.J., J.C.S.]; by the National Institute of Diabetes and Digestive and Kidney Diseases (NIDDK) Kidney Precision Medicine Project grant U2CDK114886 [K.B., E.M.Q., Y.J.]; by the Common Fund Data Ecosystem (CFDE) award OTA 20-005 OT2 OD030545 [K.B., Y.J.]; and the National Institute of Allergy and Infectious Diseases (NIAID), Department of Health and Human Services under BCBB Support Services Contract HHSN316201300006W/HHSN27200002 [K.M.B.]. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the paper. The views and conclusions contained in this document are those of the authors and should not be interpreted as representing the official policies, either expressed or implied, of the NIH.
Publisher Copyright:
© 2022, This is a U.S. Government work and not under copyright protection in the US; foreign copyright protection may apply.
PY - 2022/12
Y1 - 2022/12
N2 - Seventeen international consortia are collaborating on a human reference atlas (HRA), a comprehensive, high-resolution, three-dimensional atlas of all the cells in the healthy human body. Laboratories around the world are collecting tissue specimens from donors varying in sex, age, ethnicity, and body mass index. However, harmonizing tissue data across 25 organs and more than 15 bulk and spatial single-cell assay types poses challenges. Here, we present software tools and user interfaces developed to spatially and semantically annotate (“register”) and explore the tissue data and the evolving HRA. A key part of these tools is a common coordinate framework, providing standard terminologies and data structures for describing specimen, biological structure, and spatial data linked to existing ontologies. As of April 22, 2022, the “registration” user interface has been used to harmonize and publish data on 5,909 tissue blocks collected by the Human Biomolecular Atlas Program (HuBMAP), the Stimulating Peripheral Activity to Relieve Conditions program (SPARC), the Human Cell Atlas (HCA), the Kidney Precision Medicine Project (KPMP), and the Genotype Tissue Expression project (GTEx). Further, 5,856 tissue sections were derived from 506 HuBMAP tissue blocks. The second “exploration” user interface enables consortia to evaluate data quality, explore tissue data spatially within the context of the HRA, and guide data acquisition. A companion website is at https://cns-iu.github.io/HRA-supporting-information/.
AB - Seventeen international consortia are collaborating on a human reference atlas (HRA), a comprehensive, high-resolution, three-dimensional atlas of all the cells in the healthy human body. Laboratories around the world are collecting tissue specimens from donors varying in sex, age, ethnicity, and body mass index. However, harmonizing tissue data across 25 organs and more than 15 bulk and spatial single-cell assay types poses challenges. Here, we present software tools and user interfaces developed to spatially and semantically annotate (“register”) and explore the tissue data and the evolving HRA. A key part of these tools is a common coordinate framework, providing standard terminologies and data structures for describing specimen, biological structure, and spatial data linked to existing ontologies. As of April 22, 2022, the “registration” user interface has been used to harmonize and publish data on 5,909 tissue blocks collected by the Human Biomolecular Atlas Program (HuBMAP), the Stimulating Peripheral Activity to Relieve Conditions program (SPARC), the Human Cell Atlas (HCA), the Kidney Precision Medicine Project (KPMP), and the Genotype Tissue Expression project (GTEx). Further, 5,856 tissue sections were derived from 506 HuBMAP tissue blocks. The second “exploration” user interface enables consortia to evaluate data quality, explore tissue data spatially within the context of the HRA, and guide data acquisition. A companion website is at https://cns-iu.github.io/HRA-supporting-information/.
UR - http://www.scopus.com/inward/record.url?scp=85143842442&partnerID=8YFLogxK
U2 - 10.1038/s42003-022-03644-x
DO - 10.1038/s42003-022-03644-x
M3 - Article
C2 - 36513738
AN - SCOPUS:85143842442
SN - 2399-3642
VL - 5
JO - Communications Biology
JF - Communications Biology
IS - 1
M1 - 1369
ER -