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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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Bycom Resource Report Resource Website |
Bycom (RRID:SCR_000659) | software resource | A software which can perform methylcytosine calling from BS-seq (WGBS and RRBS), and permits either unmapped reads (FASTQ) or mapped reads (SAM/BAM) to be used as the input data. Certain SNPs (C>A/G) can also be selected in the output. | methylcytosine, bs-seq, fastq, sam, bam, snps, snp, wgbs, rrbs, sorftw |
is listed by: OMICtools has parent organization: SourceForge |
PMID:25255082 | Free, Available for download, Freely available | OMICS_00594 | SCR_000659 | 2026-08-29 11:28:14 | 0 | ||||||||
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StatTech Resource Report Resource Website 1+ mentions |
StatTech (RRID:SCR_023071) | data access protocol, software resource, web service | Web service for statistics with automated data analysis mode. | statistics, automated data analysis | Restricted | SCR_023071 | 2026-08-29 11:27:52 | 3 | |||||||||||
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Drosophila Gross Anatomy Ontology Resource Report Resource Website |
Drosophila Gross Anatomy Ontology (RRID:SCR_010311) | FB-BT | controlled vocabulary, data or information resource, ontology | A structured controlled vocabulary of the anatomy of Drosophila melanogaster. | obo |
is used by: Virtual Fly Brain is listed by: BioPortal |
nlx_157391 | SCR_010311 | 2026-08-29 11:27:53 | 0 | |||||||||
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GENERA Resource Report Resource Website 1+ mentions |
GENERA (RRID:SCR_023113) | data or information resource, narrative resource, training material, workflow | Software toolbox to infer completely reproducible comparative genomic and metabolic analyses on prokaryotes and small eukaryotes. | Genomic, Genome assembly, Phylogeny, Phylogenomic, comparative genomic, metabolic analyses, prokaryotes, eukaryotes | Free, Available for download, Freely available | SCR_023113 | GEN-ERA toolbox | 2026-08-29 11:28:24 | 9 | ||||||||||
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OncoMerge Resource Report Resource Website 1+ mentions |
OncoMerge (RRID:SCR_023079) | software resource | Software tool to integrate somatic mutation types into comprehensive integrated somatic mutation matrix for downstream analyses.Somatic mutation integration platform that tames allelic heterogeneity, discovers causal mutations, integrates binary PAM and fusion with quantitative CNA data types, and overcomes known obstacles in cancer genetics. Used for systematic integration of protein affecting mutations, gene fusions, and copy number alterations into comprehensive somatic mutational profile. | integrate somatic mutation types, comprehensive integrated somatic mutation matrix, downstream analyses, protein affecting mutations, gene fusions, copy number alterations, systematic integration, comprehensive somatic mutational profile, | DOI:10.1101/2022.07.22.501139 | Free, Available for download, Freely available | SCR_023079 | 2026-08-29 11:28:14 | 1 | ||||||||||
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ICEPO Resource Report Resource Website 1+ mentions |
ICEPO (RRID:SCR_014359) | ICEPO | controlled vocabulary, data or information resource, ontology | An ontology distributed in OWL format which contains comprehensive terms describing ion channel electrophysiology. Terms from related ontologies, such as Cell Physiology Ontology (CPO), Cardiac Electrophysiology Ontology (CEPO), and Unit Ontology, were integrated into ICEPO. | electrophysiology, ion channel, ontology, owl | Open, Available for download, Supplementary files are available to download | SCR_014359 | Ion Channel ElectroPhysiology Ontology (ICEPO), Ion Channel ElectroPhysiology Ontology | 2026-08-29 11:27:54 | 1 | |||||||||
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DistillerSR Resource Report Resource Website 10+ mentions |
DistillerSR (RRID:SCR_023078) | data management software, software application, software resource | Literature review software by DistillerSR Inc. Automates management of literature collection, screening, and assessment using AI and intelligent workflows. From systematic literature review to rapid review to living review, makes any project simpler to manage and configure to produce transparent, audit-ready, and compliant results. | DistillerSR Inc., management of literature collection, screening, and assessment, project to manage, literature review software | Restricted | SCR_023078 | 2026-08-29 11:28:14 | 11 | |||||||||||
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MS-DIAL Resource Report Resource Website 100+ mentions |
MS-DIAL (RRID:SCR_023076) | software resource | Software tool for data independent MS/MS deconvolution for comprehensive metabolome analysis. Universal program for untargeted metabolomics that supports multiple instruments (GC/MS, GC/MS/MS, LC/MS, and LC/MS/MS) and MS vendors (Agilent, Bruker, LECO, Sciex, Shimadzu, Thermo, and Waters). Used for untargeted metabolomics and lipidomics supporting any type of chromatography/mass spectrometry methods. | Data independent MS/MS deconvolution, metabolome analysis, untargeted metabolomics universal program, supports multiple instruments and MS vendors, untargeted metabolomics and lipidomics, chromatography, mass spectrometry | PMID:25938372 | Free, Available for download, Freely available | biotools:ms_dial | https://bio.tools/ms_dial, https://github.com/mtbinfo-team/mtbinfo.github.io, https://mtbinfo-team.github.io/mtbinfo.github.io/ | SCR_023076 | 2026-08-29 11:28:23 | 127 | ||||||||
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Physico-Chemical Methods and Properties Resource Report Resource Website |
Physico-Chemical Methods and Properties (RRID:SCR_010407) | FIX | controlled vocabulary, data or information resource, ontology | Two ontologies: methods and properties (but not objects, which are subject of the chemical ontology). The methods are applied to study the properties. | obo, method, property, biophysical chemistry, physico-chemical |
is listed by: BioPortal is listed by: OBO has parent organization: CHEBI |
nlx_157552 | ftp://ftp.ebi.ac.uk/pub/databases/chebi/ontology/fix.obo | SCR_010407 | 2026-08-29 11:28:15 | 0 | ||||||||
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Syndromic Surveillance Ontology Resource Report Resource Website |
Syndromic Surveillance Ontology (RRID:SCR_010409) | SSO | controlled vocabulary, data or information resource, ontology | Ontology that encodes agreement among experts about how Emergency Department (ED) chief complaints are grouped into syndromes of public health importance (consensus definitions). | owl | is listed by: BioPortal | nlx_157600 | SCR_010409 | 2026-08-29 11:27:53 | 0 | |||||||||
|
Orphanet Rare Disease Ontology Resource Report Resource Website |
Orphanet Rare Disease Ontology (RRID:SCR_010402) | ORDO | controlled vocabulary, data or information resource, ontology | Ontology to provide a structured vocabulary for rare diseases capturing relationships between diseases, genes and other relevant features which will form a useful resource for the computational analysis of rare diseases. It derived from the Orphanet database (http://www.orpha.net) , a multilingual database dedicated to rare diseases populated from literature and validated by international experts. It integrates a nosology (classification of rare diseases), relationships (gene-disease relations, epiemological data) and connections with other terminologies (MeSH, SNOMED CT, UMLS, MedDRA), databases (OMIM, UniProtKB, HGNC, ensembl, Reactome, IUPHAR, Geantlas) or classifications (ICD10). The ontology will be maintained by Orphanet and further populated with new data. Orphanet classifications can be browsed in the OLS view. The Orphanet Rare Disease Ontology is updated monthly and follows the OBO guidelines on deprecation of terms. It constitutes the official ontology of rare diseases produced and maintained by Orphanet (INSERM, US14). | owl |
is listed by: BioPortal has parent organization: Orphanet has parent organization: European Bioinformatics Institute |
Rare disease | nlx_157540 | SCR_010402 | 2026-08-29 11:27:53 | 0 | ||||||||
|
Parasite Experiment Ontology Resource Report Resource Website |
Parasite Experiment Ontology (RRID:SCR_010403) | PEO | controlled vocabulary, data or information resource, ontology | Ontology that models provenance metadata associated with experiment protocols used in parasite research. The PEO extends the upper-level Provenir ontology (http://knoesis.wright.edu/provenir/provenir.owl) to represent parasite domain-specific provenance terms. The PEO (v 1.0) includes Proteome, Microarray, Gene Knockout, and Strain Creation experiment terms along with other terms that are used in pathway. | owl | is listed by: BioPortal | nlx_157541 | SCR_010403 | 2026-08-29 11:28:23 | 0 | |||||||||
|
Pharmacogenomic Relationships Ontology Resource Report Resource Website |
Pharmacogenomic Relationships Ontology (RRID:SCR_010406) | PHARE | controlled vocabulary, data or information resource, ontology | Ontology that proposes concepts and roles to represent relationships of pharmacogenomics interest. | owl | is listed by: BioPortal | nlx_157546 | SCR_010406 | 2026-08-29 11:28:23 | 0 | |||||||||
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Online Application for Survival Analysis (OASIS) Resource Report Resource Website 10+ mentions |
Online Application for Survival Analysis (OASIS) (RRID:SCR_014450) | OASIS | software resource, web application | A tool for various statistical tasks involved in analyzing survival data which provides a uniform platform to facilitate efficient statistical analyses of survival data in the aging field. The statistical features of OASIS include the calculation of Kaplan-Meier estimates, mean/median lifespan, mortality rate, Mantel-Cox Log-Rank test, Fishers exact test, weighted Log-Rank test, Kolmogorov-Smirnov test and Neymans smooth test. Moreover, OASIS generates survival and mortality curves that can be easily exported and modified by using common graphic softwares. | statistical analysis system, web application, survival data, data analysis, aging | POSTECH BRI Grant ; National Core Research Center for Systems Bio-Dynamics 20090091509; World Class University program R31-2010-000-10100-0 |
PMID:21858155 | Source code is available, Acknowledgement required, Python must be installed | SCR_014450 | Online Application for Survival Analysis | 2026-08-29 11:28:16 | 12 | |||||||
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EvidenceFinder Resource Report Resource Website 1+ mentions |
EvidenceFinder (RRID:SCR_013764) | software resource, web application | A web application to assist in the identification of articles and research related to literature search terms. The search covers full text articles in the Europe PMC repository. Relevant papers are suggested to users based on the scientific term searched and the selection of questions, generated by the application, relevant to term searched. | web application, software resource, literature search, bio.tools |
is used by: Europe PubMed Central is listed by: Connected Researchers is listed by: Debian is listed by: bio.tools is related to: Connected Researchers is related to: Europe PubMed Central has parent organization: Europe PubMed Central |
Wellcome Trust 098231 | DOI:10.1093/nar/gku1061 | Free, Public | biotools:evidence_finder | https://bio.tools/evidence_finder | SCR_013764 | 2026-08-29 11:28:22 | 3 | ||||||
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OntoNeuroLOG Resource Report Resource Website |
OntoNeuroLOG (RRID:SCR_008957) | controlled vocabulary, data or information resource, ontology | An ontology for neuroimaging or medical imaging studies based on DOLCE (Descriptive Ontology for Linguistic and Cognitive Engineering), as the foundational ontology. Detailed description from web: Our aim is the design of a common semantic model providing a unified view on all data and tools to be shared between NeuroLOG partners. For this purpose, we built a multi-layered and multi-components formal ontology. We chose a design framework that structures the ontology at different levels of abstraction while respecting common conceptualization choices. At the highest level is a top-level ontology that includes abstract concepts and relationships valid across domains. We adopted DOLCE (Descriptive Ontology for Linguistic and Cognitive Engineering), as the foundational ontology. We then added Core ontologies, which provide generic, basic and minimal concepts and relations in a specific domain. By minimal we mean that core ontologies should include only the most reusable and widely applicable categories. These kinds of ontologies are essential for sharing intended meaning between different domains. We adopted I& DA (Information and Discourse Acts), a core ontology initially built for classifying documents as a function of their content.We use it to model medical images, which we consider as types of documents. Participant Roles is the core ontology we use to describe the modes of image participation in data processing. I& DA and Participant Roles are built according to DOLCE ontological commitments. On the basis of these two layers, we constructed our Domain ontology dedicated to conceptualizing a specific domain, in this case neuroimaging. Obviously, large domains such as neuroimaging can be divided into sub-domains for the sake of modularization. | neuroimaging, medical imaging, dicom term |
is related to: NeuroLOG has parent organization: University of Nice Sophia Antipolis; Nice; France |
PMID:18440282 | nlx_151929 | SCR_008957 | Onto Neuro Log, OntoNeuro LOG | 2026-08-29 11:28:15 | 0 | ||||||||
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Ontology for Drug Discovery Investigations Resource Report Resource Website |
Ontology for Drug Discovery Investigations (RRID:SCR_010383) | DDI | controlled vocabulary, data or information resource, ontology | Ontology for the description of drug discovery investigations. DDI aims to follow to the OBO (Open Biomedical Ontologies) Foundry principles, uses relations laid down in the OBO Relation Ontology, and be compliant with Ontology for biomedical investigations (OBI). | owl | is listed by: BioPortal | nlx_157514 | SCR_010383 | 2026-08-29 11:27:53 | 0 | |||||||||
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Ontology for Genetic Susceptibility Factor Resource Report Resource Website |
Ontology for Genetic Susceptibility Factor (RRID:SCR_010386) | OGSF | controlled vocabulary, data or information resource, ontology | Application ontology to model / represent the notion of genetic susceptibility to a specific disease or an adverse event or a pathological biological process. It is developed using BFO2.0''s framwork. The ontology is under the domain of genetic epidemiology. | owl, genetic epidemiology | is listed by: BioPortal | nlx_157518 | SCR_010386 | 2026-08-29 11:28:15 | 0 | |||||||||
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SignalP Resource Report Resource Website 10000+ mentions |
SignalP (RRID:SCR_015644) | software resource, web application | Web application for prediction of the presence and location of signal peptide cleavage sites in amino acid sequences from different organisms. The method incorporates a prediction of cleavage sites and a signal peptide/non-signal peptide prediction based on a combination of several artificial neural networks. | prediction, signal peptide, cleavage site, amino acid, sequence, artificial neural network |
is listed by: SoftCite has parent organization: DTU Center for Biological Sequence Analysis |
PMID:28451972 | Freely available, Acknowledgment requested, Free, Available for download, Runs on Windows, Runs on Mac OS | SCR_015644 | 2026-08-29 11:28:14 | 10033 | |||||||||
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Cancer Research and Management ACGT Master Ontology Resource Report Resource Website |
Cancer Research and Management ACGT Master Ontology (RRID:SCR_006953) | ACGT-MO | controlled vocabulary, data or information resource, ontology | Ontology to represent the domain of cancer research and management in a computationally tractable manner. | owl | is listed by: BioPortal | nlx_157351 | SCR_006953 | ACGT Master Ontology | 2026-08-29 11:28:23 | 0 |
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