Cross‐organism analysis using InterMine

Lyne, Rachel; Sullivan, Julie; Butano, Daniela; Contrino, Sergio; Heimbach, Joshua; Hu, Fengyuan; Kalderimis, Alex; Lyne, Mike; Smith, Richard N.; Stepan, Radek; Balakrishnan, Rama; Binkley, Gail; Harris, Todd W.; Karra, Kalpana; Moxon, Sierra; Motenko, Howie; Neuhauser, Steven B.; Ruzicka, Leyla; Cherry, J. Michael; Richardson, Joel E.; Stein, Lincoln; Westerfield, Monte; Worthey, Elizabeth A.; Micklem, Gos

doi:10.1002/dvg.22869

Cited by 32 publications

(24 citation statements)

References 43 publications

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“…InterMine is an open-source data warehouse system used for disseminating data from large, complex biological heterogeneous data sources (49). InterMine provides sophisticated web services to support denormalized query and has been used to improve query and data access to model organism databases (50) and non-model organisms (51). InterMine is a federated approach where individual databases each can adopt and populate their own object-oriented data model, but can also align on certain aspects such as having genomic data models aligned using the SO.…”

Section: Discussionmentioning

confidence: 99%

The Monarch Initiative: an integrative data and analytic platform connecting phenotypes to genotypes across species

et al. 2016

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The correlation of phenotypic outcomes with genetic variation and environmental factors is a core pursuit in biology and biomedicine. Numerous challenges impede our progress: patient phenotypes may not match known diseases, candidate variants may be in genes that have not been characterized, model organisms may not recapitulate human or veterinary diseases, filling evolutionary gaps is difficult, and many resources must be queried to find potentially significant genotype–phenotype associations. Non-human organisms have proven instrumental in revealing biological mechanisms. Advanced informatics tools can identify phenotypically relevant disease models in research and diagnostic contexts. Large-scale integration of model organism and clinical research data can provide a breadth of knowledge not available from individual sources and can provide contextualization of data back to these sources. The Monarch Initiative (monarchinitiative.org) is a collaborative, open science effort that aims to semantically integrate genotype–phenotype data from many species and sources in order to support precision medicine, disease modeling, and mechanistic exploration. Our integrated knowledge graph, analytic tools, and web services enable diverse users to explore relationships between phenotypes and genotypes across species.

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Section: Discussionmentioning

confidence: 99%

The Monarch Initiative: an integrative data and analytic platform connecting phenotypes to genotypes across species

et al. 2016

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“…Tools are emerging to allow for high-level comparison of annotated data across species at the level of the gene or phenotype. InterMine offers a platform for cross species comparison (http://intermine.org/; Lyne et al 2015). Mines have been established for several model organisms, including fly, frog, human, mouse, rat, worm, yeast and zebrafish, and for specialized research area such as mitochondrial proteomics and modENCODE data (see http://intermine.org/).…”

Section: Discussionmentioning

confidence: 99%

Naming CRISPR alleles: endonuclease-mediated mutation nomenclature across species

Knowlton

Smith

2017

Mamm Genome

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The widespread use of CRISPR/Cas and other targeted endonuclease technologies in many species has led to an explosion in the generation of new mutations and alleles. The ability to generate many different mutations from the same target sequence either by homology-directed repair with a donor sequence or non-homologous end joining-induced insertions and deletions necessitates a means for representing these mutations in literature and databases. Standardized nomenclature can be used to generate unambiguous, concise, and specific symbols to represent mutations and alleles. The research communities of a variety of species using CRISPR/Cas and other endonuclease-mediated mutation technologies have developed different approaches to naming and identifying such alleles and mutations. While some organism-specific research communities have developed allele nomenclature that incorporates the method of generation within the official allele or mutant symbol, others use metadata tags that include method of generation or mutagen. Organism-specific research community databases together with organism-specific nomenclature committees are leading the way in providing standardized nomenclature and metadata to facilitate the integration of data from alleles and mutations generated using CRISPR/Cas and other targeted endonucleases.

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“…ZebrafishMine is based on the InterMine data warehousing system and offers options for customizable searches and downloads (Lyne et al 2015; Ruzicka et al 2015). Within the ZebrafishMine interface, human disease information can be accessed using a series of predefined search templates listed in the Templates tab on the ZebrafishMine home page (Figure 5B).…”

Section: Zfin As a Resource For Zebrafish Translational Researchmentioning

confidence: 99%

Zebrafish Models of Human Disease: Gaining Insight into Human Disease at ZFIN

et al. 2017

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The Zebrafish Model Organism Database (ZFIN; https://zfin.org) is the central resource for genetic, genomic, and phenotypic data for zebrafish (Danio rerio) research. ZFIN continuously assesses trends in zebrafish research, adding new data types and providing data repositories and tools that members of the research community can use to navigate data. The many research advantages and flexibility of manipulation of zebrafish have made them an increasingly attractive animal to model and study human disease.To facilitate disease-related research, ZFIN developed support to provide human disease information as well as annotation of zebrafish models of human disease. Human disease term pages at ZFIN provide information about disease names, synonyms, and references to other databases as well as a list of publications reporting studies of human diseases in which zebrafish were used. Zebrafish orthologs of human genes that are implicated in human disease etiology are routinely studied to provide an understanding of the molecular basis of disease. Therefore, a list of human genes involved in the disease with their corresponding zebrafish ortholog is displayed on the disease page, with links to additional information regarding the genes and existing mutations. Studying human disease often requires the use of models that recapitulate some or all of the pathologies observed in human diseases. Access to information regarding existing and published models can be critical, because they provide a tractable way to gain insight into the phenotypic outcomes of the disease. ZFIN annotates zebrafish models of human disease and supports retrieval of these published models by listing zebrafish models on the disease term page as well as by providing search interfaces and data download files to access the data. The improvements ZFIN has made to annotate, display, and search data related to human disease, especially zebrafish models for disease and disease-associated gene information, should be helpful to researchers and clinicians considering the use of zebrafish to study human disease.

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Cross‐organism analysis using InterMine

Cited by 32 publications

References 43 publications

The Monarch Initiative: an integrative data and analytic platform connecting phenotypes to genotypes across species

The Monarch Initiative: an integrative data and analytic platform connecting phenotypes to genotypes across species

Naming CRISPR alleles: endonuclease-mediated mutation nomenclature across species

Zebrafish Models of Human Disease: Gaining Insight into Human Disease at ZFIN

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