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| Resource Name | Proper Citation | Abbreviations | Resource Type |
Description |
Keywords | Resource Relationships | |||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
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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 | |||||||||
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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 | ||||||||
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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 | |||||||||
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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 | ||||||||
|
ECO Resource Report Resource Website 10+ mentions |
ECO (RRID:SCR_002477) | ECO | controlled vocabulary, data or information resource, ontology | A controlled vocabulary that describes types of scientific evidence within the realm of biological research that can arise from laboratory experiments, computational methods, manual literature curation, and other means. Researchers can use these types of evidence to support assertions about research subjects that result from scientific research, such as scientific conclusions, gene annotations, or other statements of fact. ECO comprises two high-level classes, evidence and assertion method, where evidence is defined as a type of information that is used to support an assertion, and assertion method is defined as a means by which a statement is made about an entity. Together evidence and assertion method can be combined to describe both the support for an assertion and whether that assertion was made by a human being or a computer. However, ECO can not be used to make the assertion itself; for that, one would use another ontology, free text description, or other means. ECO was originally created around the year 2000 to support gene product annotation by the Gene Ontology. Today ECO is used by many groups concerned with provenance in scientific research. ECO is used in AmiGO 2 | evidence, assertion, assertion method, gene product, obo, evidence code, experiment, similarity, provenance |
is listed by: BioPortal is related to: AmiGO is related to: Gene Ontology has parent organization: University of Maryland School of Medicine; Maryland; USA has parent organization: Google Code |
NIGMS GM089636 | Free, Available for download, Freely available | nlx_155860 | http://code.google.com/p/evidenceontology/, http://bioportal.bioontology.org/ontologies/ECO | SCR_002477 | Evidence Codes Ontology, Evidence Ontology, evidenceontology, The Evidence Ontology | 2026-08-29 11:27:53 | 19 | |||||
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DynaMine Resource Report Resource Website 10+ mentions |
DynaMine (RRID:SCR_014559) | software resource, web application | An NMR based method for protein folding prediction. Users can enter a UniProt identifier, FASTA sequences, or upload a file containing FASTA sequences and results are returned., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025. | nmr, protein folding, prediction, fasta, sequence, dynamics | PMID:24225580 | THIS RESOURCE IS NO LONGER IN SERVICE | http://dynamine.ibsquare.be | SCR_014559 | 2026-08-29 11:28:22 | 44 | |||||||||
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Medical image simulation Resource Report Resource Website 1+ mentions |
Medical image simulation (RRID:SCR_010355) | OntoVIP | controlled vocabulary, data or information resource, ontology | Ontology that describes the content of the models used in medical image simulation developed in the context of the Virtual Imaging Platform project (VIP), a french project aiming at sharing medical image simulation resources. This ontology can be used to annotate such models in order to highlight the different entities that are present in the 3D scene to be imaged, i.e. anatomical structures, pathological structures, foreign bodies, contrast agents etc. The model allows also to associate to these entities information about their physical qualities, which are used in the medical image simulation process (to mimick physical phenomena involved in CT, MR, US and PET imaging). This ontology partly relies on the OntoNeuroLOG ontology (ONL-DP ONL-MR-DA), as well as PATO, RadLex, FMA and ChEBI. | owl | is listed by: BioPortal | French National Research Agency ANR-09-COSI-03 | nlx_157472 | SCR_010355 | 2026-08-29 11:27:53 | 3 | ||||||||
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Mental State Assessment Resource Report Resource Website 1+ mentions |
Mental State Assessment (RRID:SCR_010357) | ONL-MSA | controlled vocabulary, data or information resource, ontology | Ontology that is a module of the OntoNeuroLOG ontology that covers the field of mental state assessments, i.e. instruments, instrument variables, assessments, and resulting scores, developed in the context of the NeuroLOG project, a french project aiming at integrating distributed heterogeous resources in neuroimaging. It includes a generic domain core ontology, that provides a general model of such entities and a general taxonomy of behavioural, neurosychological and neuroclinical instruments, that can be easily extended to model any particular kind of instrument. It also includes such extensions for 8 relatively standard instruments, namely: (1) the Beck-depression-inventory-(BDI-II), (2) the Expanded-Disability-Status-Scale, (3) the Controlled-oral-word-association-test, (4) the Free-and-Cued-Selective-Reminding-Test-with-Immediate-Recall-16-item-version-(The-Grober-and-Buschke-test), (5) the Mini-Mental-State, (6) the Stroop-color-and-word-test, (7) the Trail-making-test-(TMT), (8) the Wechsler-Adult-Intelligence-Scale-third-edition, (9) the Clinical-Dementia-Rating-scale, (10) the Category-verbal-fluency, (11) the Rey-Osterrieth-Complex-Figure-Test-(CFT). | owl neuroimaging, mri, mental state assessment | is listed by: BioPortal | French National Research Agency ANR-06-TLOG-024 | nlx_157474 | SCR_010357 | MSA ontology | 2026-08-29 11:28:23 | 1 | |||||||
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3Omics Resource Report Resource Website 1+ mentions |
3Omics (RRID:SCR_014678) | software resource, web application | THIS RESOURCE IS NO LONGER IN SERVICE, documented October 19, 2016. A web tool for visualizing and integrating multiple inter- or intra-transcriptomic, proteomic, and metabolomic human data. 3Omics generates inter-omic correlation networks to visualize relationships in data with respect to time or experimental conditions for transcripts, proteins and metabolites. | metabolomics, metabolomics tool, transcriptomics, proteomics, inter-omic, correlation, network, relationship visualization | is listed by: Metabolomics Workbench | PMID:23875761 | THIS RESOURCE IS NO LONGER IN SERVICE | SCR_014678 | 2026-08-29 11:28:16 | 1 | |||||||||
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Metagenome Sample Vocabulary Resource Report Resource Website |
Metagenome Sample Vocabulary (RRID:SCR_010358) | MSV | controlled vocabulary, data or information resource, ontology | An ontology for metagenome sample metadata that mainly defines predicates. | owl | is listed by: BioPortal | nlx_157475 | SCR_010358 | 2026-08-29 11:28:15 | 0 | |||||||||
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Mosquito Gross Anatomy Ontology Resource Report Resource Website |
Mosquito Gross Anatomy Ontology (RRID:SCR_003839) | TGMA | controlled vocabulary, data or information resource, ontology | A structured controlled vocabulary of the anatomy of mosquitoes. | obo | is listed by: BioPortal | nlx_157485 | SCR_003839 | 2026-08-29 11:28:23 | 0 | |||||||||
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CPTAC Proteomics Pipeline Infrastructure Ontology Resource Report Resource Website |
CPTAC Proteomics Pipeline Infrastructure Ontology (RRID:SCR_006945) | CPTAC | controlled vocabulary, data or information resource, ontology | A basic ontology which describes the proteomics pipeline infrastructure for CPTAC project | owl | is listed by: BioPortal | nlx_157349 | SCR_006945 | 2026-08-29 11:28:15 | 0 | |||||||||
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GS-EM Resource Report Resource Website |
GS-EM (RRID:SCR_003992) | GS-EM | software application, software resource | Software application (entry from Genetic Analysis Software) | gene, genetic, genomic | is listed by: Genetic Analysis Software | nlx_154366 | SCR_003992 | GenoSpectrum Expectation-Maximuzation | 2026-08-29 11:30:55 | 0 |
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