Software
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.
How the layers fit together
The credit-capture pipeline
Essential infrastructure sits at both ends: one platform gives an output its first persistent, citable identity, another surfaces that identity as part of a researcher's formal academic profile. Everything between them is intermediary — the services that merge, enrich, track and standardise the record on its way across.
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.
Data
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)
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)
Training
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)
Data
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)
Software
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)
Peer review
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
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)
Software
WorkflowHub
Registry for computational workflows, providing citable, versioned identifiers.
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Currently captures credit for
- FAIR Software Release (Software)
General
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.
General
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.
General
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.
General
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.
General
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.
Software
ELIXIR Research Software Ecosystem (RSEc)
Metadata commons that unifies tool identifiers across eight software registries and cross-checks their records against each other, surfacing gaps and conflicts so a tool's description stays consistent and citable wherever it is found.
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Applicability & usability
Free and open, with all metadata version-controlled and reusable; no registration is needed to consume it. A tool only benefits if it is already described in one of the upstream registries RSEc imports from, so the practical step is getting it into bio.tools, Bioconda, Bioconductor, BioContainers, Debian Med, Galaxy Codex, OpenEBench or WorkflowHub first.
Software
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.
General
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 controlled vocabularies are the semantic layer everything else here depends on: they fix what a research activity or output is called, so a contribution recorded on one platform means the same thing on another. The vocabularies in production today are activity-centric — CRediT standardises the contributor roles behind an output rather than the output itself. The gap is output-centric: no widely adopted or established ontology for non-traditional outputs currently exists, leaving NTO types described inconsistently from platform to platform.
General
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.
External cross-walk
By CoARA OI4RRA tier
The same 18 platforms grouped by the four-tier reference architecture from the CoARA working group on Open Infrastructures for Responsible Research Assessment. This is a supplementary lens, not a replacement: each card keeps an outlined badge naming the Essential or Intermediary group it belongs to here, and each tier below names the groups its members came from. The two models deliberately disagree — CoARA's Tier 3 gathers services this registry files under three separate headings — and that divergence is the point of showing both.
Tier 0 — Foundation
Essential metadata, ensuring consistent tracking with Persistent Identifiers (PIDs), and adopting standardised protocols.
Our grouping: Ontologies & Controlled Vocabularies (Intermediary) · Academic Profiles & Representation (Essential)
Tier 0Intermediary
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.
Tier 0Essential
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.
Tier 1 — Research Publishing Venues
Repositories, open access journals and publishers where the public is accessing the research products like articles, data, software, and many others.
Our grouping: Publishing & Persistent Identifier Provision (Essential)
Tier 1Essential
bio.tools
Specialised registry assigning persistent identifiers to research software and services for discovery and reuse.
Show details
Currently captures credit for
- Research Software Code Repository (Software)
- Software Package (Software)
Tier 1Essential
DMPonline
Web-based tool for authoring, sharing, and publishing Data Management Plans against funder-specific templates, giving the DMP itself a hosted, citable record.
Show details
Currently captures credit for
- Data Management Plan (DMP) (Data)
Tier 1Essential
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.
Show details
Currently captures credit for
- FAIR Metadata Record (Data)
- Public Dataset Entry Submission (Data)
Tier 1Essential
ELIXIR TeSS
Platform for discovering and registering life-science training materials and events.
Show details
Currently captures credit for
- Training Material (Training)
- FAIR Training Material Release (Training)
- Learning Path (Training)
Tier 1Essential
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.
Show details
Currently captures credit for
- Public Data Service (Data)
Tier 1Essential
GitHub
Version-controlled code hosting; the primary home for research software repositories prior to archival/PID assignment.
Show details
Currently captures credit for
- Documentation (Software)
- Research Software Code Repository (Software)
Tier 1Essential
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.
Show details
Currently captures credit for
- Published Peer Review Report (Peer review)
Tier 1Essential
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.
Show details
Currently captures credit for
- Research Software Code Repository (Software)
Tier 1Essential
WorkflowHub
Registry for computational workflows, providing citable, versioned identifiers.
Show details
Currently captures credit for
- FAIR Software Release (Software)
Tier 1Essential
Zenodo
General-purpose repository issuing DOIs for datasets, software releases, training materials, and reports.
Show details
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)
Tier 2 — Scholarly Metadata Aggregators
Database aggregators or Scientific Knowledge Graph that contains the metadata in tiers 0 and 1.
Our grouping: Metadata Enrichment & Quality Context (Intermediary) · Aggregation & Deduplication (Intermediary)
Tier 2Intermediary
ELIXIR Research Software Ecosystem (RSEc)
Metadata commons that unifies tool identifiers across eight software registries and cross-checks their records against each other, surfacing gaps and conflicts so a tool's description stays consistent and citable wherever it is found.
Show details
Applicability & usability
Free and open, with all metadata version-controlled and reusable; no registration is needed to consume it. A tool only benefits if it is already described in one of the upstream registries RSEc imports from, so the practical step is getting it into bio.tools, Bioconda, Bioconductor, BioContainers, Debian Med, Galaxy Codex, OpenEBench or WorkflowHub first.
Tier 2Intermediary
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.
Tier 3 — Research Assessment Services
Services and platforms that are leveraging the previous tiers in order to generate metrics, analytics and indicators tailored for RRA.
Our grouping: Active Contribution Tracking (Intermediary) · Metadata Enrichment & Quality Context (Intermediary) · Academic Profiles & Representation (Essential)
Tier 3Intermediary
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.
Show details
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.
Tier 3Intermediary
BIP!
Adds impact-related annotations (e.g. topics, influence indicators) to research outputs.
Show details
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.
Tier 3Essential
BIP! Scholar
Aggregates credit-relevant data into metadata-rich, human-readable researcher profiles tailored to discipline/contribution type.
Show details
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.
Tier 3Intermediary
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.
Tier 3Essential
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.
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