Evidence map›Paper›PMID 31272389›Full record

ArticleBMC bioinformatics2019

OSCI: standardized stem cell ontology representation and use cases for stem cell investigation.

Yongqun He, William D Duncan, Daniel J Cooper, Jens Hansen, Ravi Iyengar, Edison Ong, Kendal Walker, Omar Tibi, Sam Smith, Lucas M Serra and 5 more

Open access · goldAbstract read
PubMed Full text at PMC Publisher
In one paragraph

Article in BMC bioinformatics, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 2 papers.

0numbers the graph read from it
0cells of the map it votes in
2citing papers in PubMed
0.4field-weighted citation impact, top 38% of its field
1 · What the graph read from it

What it found

Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.

The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.

2 · The registry

The trial behind it

Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.

Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.

3 · Its place in the literature

Who cites it

2 citing papers in PubMed, 5 citations in OpenAlex.

  1. Article
  2. Article
4 · The record

Corrections and comments

PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.

5 · Who and what money

Authors and funding

15 authors at 6 institutions in 1 country.

Yongqun HeUniversity of Michigan Medical School, Ann Arbor, MI, USA. yongqunh@med.umich.edu.
William D DuncanRoswell Park Comprehensive Cancer Center, Buffalo, NY, USA.
Daniel J CooperUniversity of Miami, Miami, FL, USA.
Jens HansenPharmacological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
Ravi IyengarPharmacological Sciences, Icahn School of Medicine at Mount Sinai, New York, NY, USA.
Edison OngUniversity of Michigan Medical School, Ann Arbor, MI, USA.
Kendal WalkerUniversity of Michigan Medical School, Ann Arbor, MI, USA.
Omar TibiJohn Hopkins Unversity, Baltimore, MD, USA.
Sam SmithDataSmith LLC, Detroit, MI, USA.
Lucas M SerraDepartment of Biomedical Informatics, Jacobs School of Medicine and Biomedical Sciences, University at Buffalo, Buffalo, NY, USA.
Jie ZhengUniversity of Pennsylvania, Philadelphia, PA, USA.
Sirarat SarntivijaiELIXIR, Wellcome Genome Campus, Hinxton, Cambridge, UK.
Stephan SchürerUniversity of Miami, Miami, FL, USA.
K Sue O'SheaUniversity of Michigan Medical School, Ann Arbor, MI, USA.
Alexander D DiehlDepartment of Biomedical Informatics, Jacobs School of Medicine and Biomedical Sciences, University at Buffalo, Buffalo, NY, USA. addiehl@buffalo.edu.
University of Michigan–Ann Arbor · USIcahn School of Medicine at Mount Sinai · USUniversity at Buffalo, State University of New York · USUniversity of Miami · USRoswell Park Comprehensive Cancer Center · USUniversity of Pennsylvania · US

Funding

Two-Spirit Films in Indigenous Cancer HealthP30CA016056 · NCI · ROSWELL PARK CANCER INSTITUTE CORP · PI Dean G. Tang · 1985 to 2026
$116.6M
University of Buffalo Clinical and Translational Science Institute - Supplement SchulyerUL1TR001412 · NCATS · STATE UNIVERSITY OF NEW YORK AT BUFFALO · PI MURPHY, TIMOTHY F · 2015 to 2024
$33.8M
Data Coordination and Integration Center for LINCS-BD2KU54HL127624 · NHLBI · ICAHN SCHOOL OF MEDICINE AT MOUNT SINAI · PI MA'AYAN, AVI, SCHURER, STEPHAN C · 2014 to 2019
$23.5M
Role of CACNA1C - a shared risk gene in neuropsychiatric disordersU19MH106434 · NIMH · UNIVERSITY OF PENNSYLVANIA · PI O'SHEA, K SUE SUE · 2016 to 2020
$13.8M
MOLECULAR MECHANISM OF DESENSITIZATIONR01GM054508 · NIGMS · MOUNT SINAI SCHOOL OF MEDICINE OF NYU · PI IYENGAR, SRINIVAS RAVI V · 1995 to 2016
$8.0M
Resource Dissemination and Outreach Center for Illuminating the Druggable GenomeU24TR002278 · NCATS · UNIVERSITY OF MIAMI SCHOOL OF MEDICINE · PI SCHURER, STEPHAN C, SKLAR, LARRY A. · 2018 to 2023
$3.7M
Unifying Templates, Ontologies and Tools to Achieve Effective Annotation of Bioassay ProtocolsU01LM012630 · NLM · UNIVERSITY OF MIAMI SCHOOL OF MEDICINE · PI BUNIN, BARRY A, MUSEN, MARK A · 2017 to 2020
$2.1M
NCATS NIH HHS U24 TR002278NCATS NIH HHS UL1 TR001412NCI NIH HHS P30 CA016056NHLBI NIH HHS U54 HL127624NIGMS NIH HHS R01 GM054508NIMH NIH HHS U19 MH106434NLM NIH HHS U01 LM012630
6 · The paper itself

Abstract

backgroundStem cells and stem cell lines are widely used in biomedical research. The Cell Ontology (CL) and Cell Line Ontology (CLO) are two community-based OBO Foundry ontologies in the domains of in vivo cells and in vitro cell line cells, respectively.

resultsTo support standardized stem cell investigations, we have developed an Ontology for Stem Cell Investigations (OSCI). OSCI imports stem cell and cell line terms from CL and CLO, and investigation-related terms from existing ontologies. A novel focus of OSCI is its application in representing metadata types associated with various stem cell investigations. We also applied OSCI to systematically categorize experimental variables in an induced pluripotent stem cell line cell study related to bipolar disorder. In addition, we used a semi-automated literature mining approach to identify over 200 stem cell gene markers. The relations between these genes and stem cells are modeled and represented in OSCI.

conclusionsOSCI standardizes stem cells found in vivo and in vitro and in various stem cell investigation processes and entities. The presented use cases demonstrate the utility of OSCI in iPSC studies and literature mining related to bipolar disorder.

Indexed as

Biological OntologiesAnimalsBiomedical ResearchHumansStem CellsBipolar disorderCell line ontologyCell ontologyhPSCiPSCOSCIStem cell

Identifiers

PMID31272389
PMCPMC6509805
OpenAlexW2941992511

What OpenQuestion holds

Textmetadata
LicenceCC BY
Read underepoch 390

Registered trials

None linked

Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.