ArticleF1000Research2013
Construction and accessibility of a cross-species phenotype ontology along with gene annotations for biomedical research.
Article in F1000Research, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 56 papers.
What it found
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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.
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.
Who cites it
56 citing papers in PubMed.
- Prioritizing genomic variants through neuro-symbolic, knowledge-enhanced learning.Bioinformatics (Oxford, England) · 2024Article
- The Monarch Initiative in 2024: an analytic platform integrating phenotypes, genes and diseases across species.Nucleic acids research · 2024Article
- Prenatal phenotyping: A community effort to enhance the Human Phenotype Ontology.American journal of medical genetics. Part C, Seminars in medical genetics · 2022Article
- Article
- The Xenopus phenotype ontology: bridging model organism phenotype data to human health and development.BMC bioinformatics · 2022Article
- Establishment and application of information resource of mutant mice in RIKEN BioResource Research Center.Laboratory animal research · 2021Review
- Towards semantic interoperability: finding and repairing hidden contradictions in biomedical ontologies.BMC medical informatics and decision making · 2020Article
- Transforming the study of organisms: Phenomic data models and knowledge bases.PLoS computational biology · 2020Review
- Semantic characterization of adverse outcome pathways.Aquatic toxicology (Amsterdam, Netherlands) · 2020Article
- Formal axioms in biomedical ontologies improve analysis and interpretation of associated data.Bioinformatics (Oxford, England) · 2020Article
- The Monarch Initiative in 2019: an integrative data and analytic platform connecting phenotypes to genotypes across species.Nucleic acids research · 2020Article
- Xrare: a machine learning method jointly modeling phenotypes and genetic evidence for rare disease diagnosis.Genetics in medicine : official journal of the American College of Medical Genetics · 2019Article
- PathoPhenoDB, linking human pathogens to their phenotypes in support of infectious disease research.Scientific data · 2019Article
- Quantitative evaluation of ontology design patterns for combining pathology and anatomy ontologies.Scientific reports · 2019Article
- DeepPVP: phenotype-based prioritization of causative variants using deep learning.BMC bioinformatics · 2019Article
- Ontology-based semantic mapping of chemical toxicities.Toxicology · 2019Article
- Representing glycophenotypes: semantic unification of glycobiology resources for disease discovery.Database : the journal of biological databases and curation · 2019Review
- Ontology based text mining of gene-phenotype associations: application to candidate gene prediction.Database : the journal of biological databases and curation · 2019Article
- Model organism data evolving in support of translational medicine.Lab animal · 2018Review
- The anatomy of phenotype ontologies: principles, properties and applications.Briefings in bioinformatics · 2018Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
12 authors.
Funding
Abstract
Phenotype analyses, e.g. investigating metabolic processes, tissue formation, or organism behavior, are an important element of most biological and medical research activities. Biomedical researchers are making increased use of ontological standards and methods to capture the results of such analyses, with one focus being the comparison and analysis of phenotype information between species. We have generated a cross-species phenotype ontology for human, mouse and zebrafish that contains classes from the Human Phenotype Ontology, Mammalian Phenotype Ontology, and generated classes for zebrafish phenotypes. We also provide up-to-date annotation data connecting human genes to phenotype classes from the generated ontology. We have included the data generation pipeline into our continuous integration system ensuring stable and up-to-date releases. This article describes the data generation process and is intended to help interested researchers access both the phenotype annotation data and the associated cross-species phenotype ontology. The resource described here can be used in sophisticated semantic similarity and gene set enrichment analyses for phenotype data across species. The stable releases of this resource can be obtained from http://purl.obolibrary.org/obo/hp/uberpheno/.
Identifiers
What OpenQuestion holds
Registered trials
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.