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A directory of tools, AI models, datasets, and research resources for biotech, bioinformatics, and other scientific fields. Aggregated from curated GitHub awesome-lists, HuggingFace, bio.tools, Bioconductor, and more.

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The Library of Congress Linked Data Service (id.loc.gov) provides interactive and machine access to the Library's authority and bibliographic metadata, along with commonly-found standards and vocabularies used and/or maintained by the Library of Congress. Each controlled vocabulary list has a resolvable URI, as does each data value within it. Ontologies for several major data element sets are also available. This includes the LCSH (Library of Congress Subject Headings), the TGM (Thesaurus for Graphic Materials), preservation vocabularies, language and country codes, or the American Folklore Society Ethnographic Thesaurus (AFS Ethnographic Thesaurus) among others.

Loterre (Linked open terminology resources) is a platform for multidisciplinary terminological scientific resources sharing, complying with the linked open data standards and the FAIR principles.

A vocabulary in LOV gathers definitions of a set of classes and properties (together simply called terms of the vocabulary), useful to describe specific types of things, or things in a given domain or industry, or things at large but for a specific usage. Terms of vocabularies also provide the links in linked data, in the above case between a Person and a City. The definitions of terms provided by the vocabularies bring clear semantics to descriptions and links, thanks to the formal language they use (some dialect of RDF such as RDFS or OWL). In short, vocabularies provide the semantic glue enabling Data to become meaningful Data. [from https://lov.linkeddata.es/dataset/lov/about]

Identifiers correspond to literature references for molecular glue studies in the MGTbind database.

Identifiers correspond to ternary complex interactions involving molecular glues with bioactivity measurements in the MGTbind database.

Identifiers correspond to curated molecular glue compounds with chemical structures and physicochemical properties in the MGTbind database.

MoonProt provides identifiers for manually curated moonlighting proteins, which are proteins that perform two or more distinct, unrelated physiological functions using a single polypeptide chain.

Nbvok is the vocabulary service provided by the National Library of Norway, containing controlled vocabularies represented as open linked data according to the SKOS-ontology. Our vocabularies are published using the Skosmos application. SKOSMOS is developed by the National Library of Finland and designed particularly with user-friendly navigation in structured vocabularies in mind. [from about page]

The Ontology Lookup Service (OLS) is a repository for biomedical ontologies that aims to provide a single point of access to the latest ontology versions.

A mid-level ontology describing devices, services, and networking that extends SAREF

Ontobee is aimed to facilitate ontology data sharing, visualization, query, integration, and analysis.

A vocabulary of licenses produced by the Open Source Initiative (OSI)

The legacy namespace for representing OWL in XML

TyPon provides a comprehensive description of the existing microbial typing methods for the identification of bacterial Isolates and their classification. Such a description constitutes an universal format for the exchange of information on the microbial typing field, providing a vehicle for the integration of the numerous disparate online databases. In its current version, TyPon describes most used microbial typing methods but it is, and always will be, a work in progress given the constant advances in the microbial typing field.

Identifiers correspond to pangenome IDs for linking orthologous genes across Streptococcus pneumoniae strains for comparative genomics analysis

A web-developer centric archive of prefixes and URI prefixes

Identifiers correspond to systematic review protocols for the purpose of promoting transparency and reducing duplication in health research in the PROSPERO registry, an international prospective register of systematic reviews.

Raras is an open, FAIR-compliant knowledge graph of rare diseases — the largest in Latin America — integrating Orphanet, the Human Phenotype Ontology (HPO), OMIM, MONDO, ClinVar, Open Targets, PubMed and ClinicalTrials.gov with Brazilian public-health (SUS) data. It mints stable RARAS identifiers for diseases, reference centers, protocols, associations, communities and medications, each resolvable as Linked Data (SPARQL, RDF, GraphQL, GA4GH Beacon/Phenopackets) with a dereferenceable vocabulary and VOID/DCAT metadata.

Classes of the Raras rare disease knowledge graph

Properties of the Raras rare disease knowledge graph

The Registered Organization Vocabulary is a profile of the Organization Ontology for describing organizations that have gained legal entity status through a formal registration process, typically in a national or regional register.

An core data schema for the mart Connected Supplier Network (SCSN).

A representation of orders (i.e. transactions)

A symbol for a molecule in the C. elegans Small Molecule Identifier Data. Note that this isn't the same as the 'DB info' identifier

The Solid Terms vocabulary defines terms referenced in Solid specifications.

An RDF Schema that can be used to attach constraints and rules to RDFS classes, and to encapsulate reusable SPARQL queries into functions and templates.

Vocabularies useful for the Social Sciences and Humanities OpenCloud (SSHOC) project

This is not part of the W3C SWRL specification. It defines annotation properties and implementation-specific extensions (such as rule metadata, enable/disable flags, authorship, and other editor-related annotations) used by Protégé and SWRLAPI rather than the SWRL language itself.

Built-in operations for Semantic Web Rule Language (SWRL)

A local copy of the XML schema

The Odysseus dynamic Energy Profile Card (dEPC) Ontology (or the Odysseus "Energy Ontology" in short) is an advanced open semantic information structure covering a wide variety of information types relevant for improved (fossil) energy - efficiency and CO2 reduction in city's neighbourhoods. The ontology covers entities like buildings where people perform activities; but also street lighting sections, windmill parks, solar parks etc., all under the required indoor/outdoor climate conditions. (text from https://studyres.com/doc/2789908/odysseus_depc-ontology)

proposed extensions to saref4bldf

This ontology extension was created to address the following needs: - The necessity of expressing time-series of data for various tasks and services in InterConnect - A workable and unambiguous characterization of quantities, combining units with measurements. This characterization should be technically complete so that quantities cannot be confused during data exchange between unfamiliar services

Requirements from Interconnect Project -- Extensions to s4ener:Device

The flexibility ontology module (ic-flex) is by design tightly integrated with SAREF, SAREF4ENER and the following InterConnect modules: power limit (ic-pwlm), incentive table (ic-inc), S2 (ic-s2), data-point (ic-data) and forecast (ic-fc) The main concept of the ic-flex module is the ic-flex:FlexOffer, which allows to represent a flexibility offer (or schedule) as a combination of multiple time-series, data-points and forecasts. (from ontology)

This ontology extension was created to address the following need: - A clear characterization of most common forecasting data. A distinction is needed between point forecasts versus stochastic forecasts, as well as the various ways to express stochastic forecasts. The forecasted data is expressed in terms of time series. It reuses the ic-data ontology, which defines timeseries and datapoints that are important elements of forecasting. It reuses also the ic-topology ontology, which defines location (geographical but also topological, for example, the gird segment).

Ontology for the TNO interconnect project describing incentives

A schema for representing power limits and switches

This ontology covers the requirements of S2 and SPINE specifications which define Energy Flexibility. This ontology uses entities from powerLimit and incentive ontologies. Also existing standards saref and s4ener are imported for reuse and extention.

It is used to define the topological location (e.g., grid segment, market segment, regulation zone, ...) associated to a Forecast, a Timeseries or a DataPoint. It speciies where a measurement was made, for example a forecast might be valid for a specific region or grid segment.

Extension of the Ontology of Units of Measure (OM) with common units used in the Interconnect project

A schema describing users in Interconnect

This ontology captures several types of explanation that occur in the literature on explainable machine learning, Bayesian networks and rule-based expert systems. Each explanation consists of an explanandum (that which has to be explained) and an explanans (the part that performs the explaining the explanandum). The explanandum is usually just a fact, or more generally an event. The explanans can take multiple forms: set of facts combined with a rule, a set of important features, a prototype, etc, or a combination of those. (from ontology)

An ontology that encodes the Ploutos Common Semantic Model (PCSM)