bio.tools
Specialised registry assigning persistent identifiers to research software and services for discovery and reuse.
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Currently captures credit for
- Research Software Code Repository (Software)
- Software Package (Software)
Credit-capture infrastructure
Non-Traditional Output Infrastructure
The platforms that turn output-level effort into machine-readable, citable credit — from persistent identifiers to granular contribution tracking to aggregated researcher profiles.
Essential
Essential Infrastructure
The baseline layer without which non-traditional outputs cannot be credited at all: platforms that give an output its first persistent, discoverable identity, and systems that surface that identity as part of a researcher's formal academic profile.
Publishing & Persistent Identifier Provision
These platforms provide the initial repository registration for NTOs and assign the unique persistent identifiers (PIDs) necessary for their discovery, metadata hosting, and subsequent citation.
DMPonline
Web-based tool for authoring, sharing, and publishing Data Management Plans against funder-specific templates, giving the DMP itself a hosted, citable record.
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Currently captures credit for
- Data Management Plan (DMP) (Data)
ELIXIR EDD (ELIXIR Deposition Databases)
ELIXIR-recommended portfolio of trustworthy public deposition databases for biomolecular data, giving submitted datasets a discoverable, FAIR-compliant home with standardised metadata.
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Currently captures credit for
- FAIR Metadata Record (Data)
- Public Dataset Entry Submission (Data)
ELIXIR TeSS
Platform for discovering and registering life-science training materials and events.
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Currently captures credit for
- Training Material (Training)
- FAIR Training Material Release (Training)
- Learning Path (Training)
FAIRsharing
Curated registry of data and metadata standards, databases, and repositories, giving each a discoverable, citable record independent of where the underlying data is hosted.
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Currently captures credit for
- Public Data Service (Data)
GitHub
Version-controlled code hosting; the primary home for research software repositories prior to archival/PID assignment.
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Currently captures credit for
- Documentation (Software)
- Research Software Code Repository (Software)
PREreview
Open-source, journal-independent platform for publishing community reviews of preprints, giving each review a citable, publicly discoverable record tied to the reviewer's ORCID.
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Currently captures credit for
- Published Peer Review Report (Peer review)
Software Heritage
Archives public source code at scale and assigns permanent SWHIDs (an ISO/IEC-standardised identifier scheme), preserving research software even after its original hosting location disappears.
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Currently captures credit for
- Research Software Code Repository (Software)
WorkflowHub
Registry for computational workflows, providing citable, versioned identifiers.
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Currently captures credit for
- FAIR Software Release (Software)
Zenodo
General-purpose repository issuing DOIs for datasets, software releases, training materials, and reports.
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Currently captures credit for
- Data Management Plan (DMP) (Data)
- FAIR Training Material Release (Training)
- FAIR Software Release (Software)
- Software Management Plan (Software)
- Strategy Document (Research support)
- Event Output (Agenda / Proceedings / Report) (Research support)
- Policy Brief (Research support)
- Host for digital NTOs (General)
Academic Profiles & Representation
These systems aggregate data from primary NTO repositories, enriched metadata services, and active tracking platforms to comprehensively host and represent PID-associated NTOs — translating granular research activity into meaningful, human-readable profiles suitable for formal academic assessment.
BIP! Scholar
Aggregates credit-relevant data into metadata-rich, human-readable researcher profiles tailored to discipline/contribution type.
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Applicability & usability
Profiles are generated automatically from OpenAIRE Graph data for any researcher with a discoverable output record — no registration or manual curation required, but coverage is limited to what's already indexed upstream.
ORCID
Persistent researcher identifier used to link contributions of any kind back to an individual across systems.
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Applicability & usability
Free for researchers to register and keep for life; once linked, it works passively — connected publishers, funders, and repositories push updates to the profile automatically without further manual entry.
Intermediary
Intermediary Infrastructure
The layer that sits between raw publishing and the researcher's profile: aggregating records to avoid double-counting, enriching them with quality context, tracking granular ongoing labour, and providing the shared vocabularies that let all of the above interoperate.
Aggregation & Deduplication
Aggregation services merge PID-assigned NTO metadata from diverse repositories into a unified, searchable knowledge graph — essential for deduplicating records to prevent double-counting across platforms, so that clean, verified data feeds into academic profiling systems.
OpenAIRE Graph
Merges PID-assigned research output information from diverse sources into a single, searchable knowledge graph.
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Applicability & usability
Free and openly queryable via API or bulk dataset download; nothing to register. Coverage depends entirely on upstream infrastructure, though — a record only appears once its source repository already exposes a compatible PID and metadata.
Metadata Enrichment & Quality Context
These services enrich basic NTO metadata by appending missing annotations, such as specific topics or technical performance indicators — contextual enrichment that is crucial for establishing the qualitative value of NTOs and helping to prevent a quantity-over-quality assessment model.
BIP!
Adds impact-related annotations (e.g. topics, influence indicators) to research outputs.
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Applicability & usability
Free API and bulk downloads keyed by DOI, usable by any service that can look up a DOI — no account needed. Indicators are only computed for outputs that already have a DOI and an established citation trail.
OpenEBench
Adds software quality and benchmarking performance indicators to research software entries.
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Applicability & usability
Free to use, but enrichment isn't automatic on sign-up: a tool needs to be registered in bio.tools and its maintainers need to opt it into a benchmarking community/challenge before performance indicators appear.
Active Contribution Tracking
Active tracking platforms capture granular NTO contributions at scale through dynamic recognition models — essential for recording vital, ongoing research labour (e.g. curation) that holds significant aggregate value but remains entirely invisible within publications.
APICURON
Captures granular biocuration and annotation events using a dynamic model of entity, activity, agent, and timeline, with badges/leaderboards for visibility. Resources can also register new curation activities directly on the platform, giving it a registration role alongside its tracking function.
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Applicability & usability
Free and open source, but not self-service for end users: a database has to implement APICURON's reporting API to log its curation events before any of its individual curators can be credited, so it requires integration work on the data provider's side first.
Ontologies & Controlled Vocabularies
Structured ontologies and fixed vocabularies provide the essential semantic foundation for system interoperability, enabling highly granular, machine-readable specifications so data flows cohesively between credit-capture platforms. A major gap remains, however: dedicated NTO ontologies barely exist yet.
CRediT (Contributor Roles Taxonomy)
NISO-standardised taxonomy of contributor roles providing the shared, machine-readable vocabulary that lets credit-capture platforms describe contributions consistently.
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Applicability & usability
Free, open taxonomy — not a platform to register with. It only takes effect where a journal or submission system has integrated it into its workflow, so applicability depends on adoption upstream, not on the individual contributor.
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