Bibliographic Sources Catalog

This document lists all potential academic sources for atlas-citations, with their current status and the strategy for building their OpenAPI spec.

See also: Entities and Fields Reference for complete details on objects and attributes retrievable per source.

Overview

┌─────────────────────────────────────────────────────────────────────────────┐
│                      BIBLIOGRAPHIC SOURCES                                   │
├─────────────────────────────────────────────────────────────────────────────┤
│                                                                              │
│  PRIORITY 1 (Implemented)              PRIORITY 2 (Planned)                 │
│  ─────────────────────────             ────────────────────────             │
│  ✅ OpenAlex                           📋 Semantic Scholar                  │
│  ✅ Crossref                           📋 PubMed/NCBI                       │
│  ✅ HAL                                📋 Unpaywall                         │
│  ✅ ArXiv                              📋 OpenCitations                     │
│  ✅ ORCID                                                                    │
│                                                                              │
│  PRIORITY 3 (Extensions)               PRIORITY 4 (Specialized)             │
│  ───────────────────────               ─────────────────────────            │
│  📋 Europe PMC                         📋 DBLP                              │
│  📋 DataCite                           📋 RePEc                             │
│  📋 DOAJ                               📋 SSRN                              │
│  📋 Zenodo                             📋 bioRxiv/medRxiv                   │
│                                                                              │
│  PAID SOURCES                          REGIONAL SOURCES                     │
│  ────────────────                      ──────────────────                   │
│  💰 Scopus                             🌍 CNKI (China)                      │
│  💰 Web of Science                     🌍 CiNii (Japan)                     │
│  💰 IEEE Xplore                        🌍 SciELO (Latin America)            │
│  💰 Dimensions                         🌍 CORE (UK)                         │
│                                                                              │
└─────────────────────────────────────────────────────────────────────────────┘

Legend

Symbol	Meaning
✅	Implemented (Priority 1)
📋	Planned
💰	Paid API
🌍	Regional source
✅ OpenAPI	Official OpenAPI spec available
⚠️ OpenAPI	Partial or unmaintained spec
❌ OpenAPI	No OpenAPI spec

Major Academic Sources (Free)

Semantic Scholar

Aspect	Detail
URL	`https://api.semanticscholar.org`
Operator	Allen Institute for AI
Coverage	200M+ articles, all disciplines
OpenAPI	✅ Yes
Auth	API key recommended (free)
Rate limit	100 req/5min (without key), 1 req/sec (with key)
Format	JSON
Priority	⭐⭐⭐ High

Strengths:

Very rich citation graph
SPECTER embeddings for semantic similarity
S2ORC dataset accessible
Excellent AI/ML coverage

Alpha construction:

bash

# Retrieve the official OpenAPI spec
atlas-openapi-validator fetch \
  https://api.semanticscholar.org/api-docs/openapi.json \
  --output specs/alpha/semantic-scholar-2025-01.yaml \
  --format yaml \
  --set-stage alpha

# Validate and adapt
atlas-openapi-validator validate specs/alpha/semantic-scholar-2025-01.yaml \
  --base-url https://api.semanticscholar.org/graph/v1 \
  --headers "x-api-key=${S2_API_KEY}" \
  --output reports/semantic-scholar-alpha.json

Existing spec: https://api.semanticscholar.org/api-docs/

PubMed / NCBI E-utilities

Aspect	Detail
URL	`https://eutils.ncbi.nlm.nih.gov/entrez/eutils/`
Operator	NIH / NLM
Coverage	35M+ biomedical citations
OpenAPI	⚠️ Partial
Auth	API key recommended (free)
Rate limit	3 req/sec (without key), 10 req/sec (with key)
Format	XML, JSON (partial)
Priority	⭐⭐⭐ High

Strengths:

Absolute reference in biomedicine
MeSH terms for classification
Links to full text (PMC)
Clinical data (ClinicalTrials.gov)

Alpha construction:

bash

# No complete OpenAPI spec, build from documentation
atlas-openapi-validator scaffold \
  --name pubmed \
  --base-url https://eutils.ncbi.nlm.nih.gov/entrez/eutils \
  --output specs/alpha/pubmed-2025-01.yaml

# Main endpoints to document
# - esearch.fcgi : Search
# - efetch.fcgi : Retrieval
# - einfo.fcgi : Database metadata
# - elink.fcgi : Links between databases

# Infer schemas from responses
atlas-openapi-validator infer \
  --base-url https://eutils.ncbi.nlm.nih.gov/entrez/eutils \
  --endpoints esearch.fcgi,efetch.fcgi \
  --params "db=pubmed&retmode=json" \
  --sample-size 50 \
  --merge-into specs/alpha/pubmed-2025-01.yaml

Documentation: https://www.ncbi.nlm.nih.gov/books/NBK25500/

Europe PMC

Aspect	Detail
URL	`https://www.ebi.ac.uk/europepmc/webservices/rest/`
Operator	EMBL-EBI
Coverage	40M+ articles, European focus
OpenAPI	✅ Yes
Auth	None
Rate limit	Not officially documented
Format	JSON, XML
Priority	⭐⭐ Medium

Strengths:

Aggregates PubMed + European sources
Open Access full text
Text-mining annotations
Grant information

Alpha construction:

bash

# Spec available but needs adaptation
curl -o specs/alpha/europepmc-raw.json \
  "https://www.ebi.ac.uk/europepmc/webservices/rest/swagger.json"

atlas-openapi-validator transform specs/alpha/europepmc-raw.json \
  --output specs/alpha/europepmc-2025-01.yaml \
  --format yaml \
  --set-stage alpha

Documentation: https://europepmc.org/RestfulWebService

Unpaywall

Aspect	Detail
URL	`https://api.unpaywall.org/v2/`
Operator	OurResearch
Coverage	30M+ DOIs with OA status
OpenAPI	❌ No
Auth	Email required (parameter)
Rate limit	100k req/day
Format	JSON
Priority	⭐⭐⭐ High

Strengths:

Finds Open Access versions
Easy integration (by DOI)
License data
Direct PDF URLs

Alpha construction:

bash

# Build from documentation + inference
atlas-openapi-validator scaffold \
  --name unpaywall \
  --base-url https://api.unpaywall.org/v2 \
  --output specs/alpha/unpaywall-2025-01.yaml

# Single simple endpoint
# GET /{doi}?email=your@email.com

atlas-openapi-validator infer \
  --base-url https://api.unpaywall.org/v2 \
  --endpoints "/{doi}" \
  --sample-dois "10.1038/nature12373,10.1126/science.1157784" \
  --params "email=test@example.com" \
  --merge-into specs/alpha/unpaywall-2025-01.yaml

Documentation: https://unpaywall.org/products/api

Example spec:

yaml

openapi: '3.1.0'
info:
  title: Unpaywall API
  version: '2'
  x-atlas-metadata:
    stage: alpha
    origin:
      type: documentation
      urls:
        - https://unpaywall.org/products/api

servers:
  - url: https://api.unpaywall.org/v2

paths:
  /{doi}:
    get:
      operationId: getByDoi
      parameters:
        - name: doi
          in: path
          required: true
          schema:
            type: string
          example: '10.1038/nature12373'
        - name: email
          in: query
          required: true
          schema:
            type: string
            format: email
      responses:
        '200':
          content:
            application/json:
              schema:
                $ref: '#/components/schemas/Work'

components:
  schemas:
    Work:
      type: object
      properties:
        doi:
          type: string
        is_oa:
          type: boolean
        oa_status:
          type: string
          enum: [gold, green, hybrid, bronze, closed]
        best_oa_location:
          $ref: '#/components/schemas/OaLocation'
        oa_locations:
          type: array
          items:
            $ref: '#/components/schemas/OaLocation'

    OaLocation:
      type: object
      properties:
        url:
          type: string
          format: uri
        url_for_pdf:
          type: string
          format: uri
          nullable: true
        host_type:
          type: string
          enum: [publisher, repository]
        license:
          type: string
          nullable: true
        version:
          type: string
          enum: [publishedVersion, acceptedVersion, submittedVersion]

OpenCitations

Aspect	Detail
URL	`https://opencitations.net/`
Operator	University of Bologna
Coverage	1.4B+ citations
OpenAPI	✅ Yes
Auth	None
Rate limit	Not documented
Format	JSON, CSV
Priority	⭐⭐⭐ High

Strengths:

Open citation graph
COCI (Crossref), POCI (PubMed) data
Simple REST API
Bulk download available

Alpha construction:

bash

# API documentation available
atlas-openapi-validator scaffold \
  --name opencitations \
  --base-url https://opencitations.net/index/api/v2 \
  --from-docs https://opencitations.net/index/api/v2 \
  --output specs/alpha/opencitations-2025-01.yaml

# Main endpoints
# - /references/{doi} : Outgoing citations
# - /citations/{doi} : Incoming citations
# - /metadata/{doi} : Metadata

Documentation: https://opencitations.net/index/api/v2

DataCite

Aspect	Detail
URL	`https://api.datacite.org/`
Operator	DataCite
Coverage	50M+ DOIs (datasets, software)
OpenAPI	✅ Yes
Auth	None (read)
Rate limit	Not documented
Format	JSON:API
Priority	⭐⭐ Medium

Strengths:

DOIs for research data
DataCite Schema metadata
Data-publications links
Usage statistics

Alpha construction:

bash

# OpenAPI spec available
atlas-openapi-validator fetch \
  https://api.datacite.org/openapi \
  --output specs/alpha/datacite-2025-01.yaml \
  --set-stage alpha

# Note: JSON:API format, requires adaptation

Documentation: https://support.datacite.org/docs/api

DOAJ (Directory of Open Access Journals)

Aspect	Detail
URL	`https://doaj.org/api/`
Operator	DOAJ
Coverage	20k+ OA journals, 9M+ articles
OpenAPI	✅ Yes
Auth	API key for write
Rate limit	Not documented
Format	JSON
Priority	⭐⭐ Medium

Strengths:

Reference for Open Access journals
DOAJ quality criteria
Detailed journal metadata
APC status (publication fees)

Alpha construction:

bash

# Swagger available
atlas-openapi-validator fetch \
  https://doaj.org/api/docs/swagger.json \
  --output specs/alpha/doaj-2025-01.yaml \
  --set-stage alpha

Documentation: https://doaj.org/api/docs

Zenodo

Aspect	Detail
URL	`https://zenodo.org/api/`
Operator	CERN
Coverage	3M+ records (data, software, publications)
OpenAPI	✅ Yes
Auth	Token for write
Rate limit	60 req/min (anonymous), 100 req/min (auth)
Format	JSON
Priority	⭐⭐ Medium

Strengths:

General European repository
Automatic versioning
GitHub integration
Automatic DOIs

Alpha construction:

bash

# Spec available
atlas-openapi-validator fetch \
  https://zenodo.org/api/swagger.json \
  --output specs/alpha/zenodo-2025-01.yaml \
  --set-stage alpha

Documentation: https://developers.zenodo.org/

Specialized Sources (Free)

DBLP (Computer Science)

Aspect	Detail
URL	`https://dblp.org/`
Operator	Schloss Dagstuhl
Coverage	6M+ CS publications
OpenAPI	❌ No
Auth	None
Rate limit	Not documented
Format	XML, JSON
Priority	⭐⭐ Medium (CS)

Strengths:

Reference in computer science
Very complete conference data
Excellent author disambiguation
Simple API

Alpha construction:

bash

# Build from documentation
atlas-openapi-validator scaffold \
  --name dblp \
  --base-url https://dblp.org \
  --output specs/alpha/dblp-2025-01.yaml

# Endpoints
# - /search/publ/api : Publication search
# - /search/author/api : Author search
# - /pid/{pid}.xml : Publication by ID

atlas-openapi-validator infer \
  --base-url https://dblp.org \
  --endpoints /search/publ/api,/search/author/api \
  --response-format json \
  --sample-size 50 \
  --merge-into specs/alpha/dblp-2025-01.yaml

Documentation: https://dblp.org/faq/How+to+use+the+dblp+search+API.html

RePEc (Economics)

Aspect	Detail
URL	`https://ideas.repec.org/api.html`
Operator	RePEc
Coverage	4M+ economics working papers
OpenAPI	❌ No
Auth	None
Rate limit	Not documented
Format	JSON, XML
Priority	⭐ Low (specialized)

Strengths:

Reference in economics
Working papers and preprints
Author/institution rankings
Citations

Alpha construction:

bash

# Limited API, mainly structured scraping
atlas-openapi-validator scaffold \
  --name repec \
  --base-url https://api.repec.org \
  --output specs/alpha/repec-2025-01.yaml

# Very limited documentation

Documentation: https://ideas.repec.org/api.html

Aspect	Detail
URL	`https://www.ssrn.com/`
Operator	Elsevier
Coverage	1M+ social sciences preprints
OpenAPI	❌ No
Auth	Account required
Rate limit	Strict (anti-scraping)
Format	HTML (no public API)
Priority	⭐ Low

Strengths:

Social sciences/law/economics preprints
High downloads

Alpha construction:

⚠️ No official public API
Options:
1. Access via OpenAlex/Crossref (metadata)
2. Negotiate institutional access
3. Not recommended for atlas-citations

bioRxiv / medRxiv

Aspect	Detail
URL	`https://api.biorxiv.org/`
Operator	Cold Spring Harbor Laboratory
Coverage	250k+ biology/medicine preprints
OpenAPI	❌ No
Auth	None
Rate limit	Not documented
Format	JSON
Priority	⭐⭐ Medium

Strengths:

Biology/medicine preprints
Exhaustive COVID-19 data
Links to final publications
Simple and documented API

Alpha construction:

bash

# Documented API but no spec
atlas-openapi-validator scaffold \
  --name biorxiv \
  --base-url https://api.biorxiv.org \
  --output specs/alpha/biorxiv-2025-01.yaml

# Endpoints
# - /details/{server}/{interval} : Details by period
# - /pubs/{server}/{interval} : Publications
# - /publisher/{prefix}/{interval} : By publisher

atlas-openapi-validator infer \
  --base-url https://api.biorxiv.org \
  --endpoints /details/biorxiv/2024-01-01/2024-01-31 \
  --sample-size 100 \
  --merge-into specs/alpha/biorxiv-2025-01.yaml

Documentation: https://api.biorxiv.org/

Example spec:

yaml

openapi: '3.1.0'
info:
  title: bioRxiv/medRxiv API
  version: '2025-01'

servers:
  - url: https://api.biorxiv.org

paths:
  /details/{server}/{interval}:
    get:
      operationId: getDetails
      parameters:
        - name: server
          in: path
          required: true
          schema:
            type: string
            enum: [biorxiv, medrxiv]
        - name: interval
          in: path
          required: true
          description: Date range (YYYY-MM-DD/YYYY-MM-DD) or cursor
          schema:
            type: string
        - name: cursor
          in: query
          schema:
            type: integer
      responses:
        '200':
          content:
            application/json:
              schema:
                $ref: '#/components/schemas/DetailsResponse'

components:
  schemas:
    DetailsResponse:
      type: object
      properties:
        collection:
          type: array
          items:
            $ref: '#/components/schemas/Preprint'
        messages:
          type: array
          items:
            type: object
            properties:
              status:
                type: string
              count:
                type: integer
              total:
                type: integer

    Preprint:
      type: object
      properties:
        doi:
          type: string
        title:
          type: string
        authors:
          type: string
        author_corresponding:
          type: string
        author_corresponding_institution:
          type: string
        date:
          type: string
          format: date
        version:
          type: string
        type:
          type: string
        license:
          type: string
        category:
          type: string
        jatsxml:
          type: string
          format: uri
        abstract:
          type: string
        published:
          type: string
          description: DOI of published version if exists

Regional Sources

CNKI (China National Knowledge Infrastructure)

Aspect	Detail
URL	`https://www.cnki.net/`
Operator	Tsinghua University
Coverage	Chinese publications
OpenAPI	❌ No
Auth	Institutional subscription
Rate limit	Strict
Format	Proprietary
Priority	⭐ Low

Alpha construction:

⚠️ No public API
Access only via institutional subscription
Not recommended for atlas-citations open source

CiNii (Japan)

Aspect	Detail
URL	`https://cir.nii.ac.jp/`
Operator	NII (Japan)
Coverage	Japanese publications
OpenAPI	⚠️ Partial
Auth	Free API key
Rate limit	Not documented
Format	JSON, RDF
Priority	⭐ Low

Alpha construction:

bash

# Documented API
atlas-openapi-validator scaffold \
  --name cinii \
  --base-url https://cir.nii.ac.jp \
  --output specs/alpha/cinii-2025-01.yaml

# Requires registration for API key

Documentation: https://support.nii.ac.jp/en/cir/api/a_opensearch

SciELO (Latin America)

Aspect	Detail
URL	`https://search.scielo.org/`
Operator	FAPESP (Brazil)
Coverage	Latin American publications
OpenAPI	❌ No
Auth	None
Rate limit	Not documented
Format	JSON
Priority	⭐ Low

Alpha construction:

bash

# Solr-based API
atlas-openapi-validator scaffold \
  --name scielo \
  --base-url https://search.scielo.org/api/v1 \
  --output specs/alpha/scielo-2025-01.yaml

atlas-openapi-validator infer \
  --base-url https://search.scielo.org/api/v1 \
  --sample-size 50 \
  --merge-into specs/alpha/scielo-2025-01.yaml

CORE (UK Aggregator)

Aspect	Detail
URL	`https://api.core.ac.uk/v3/`
Operator	Open University (UK)
Coverage	300M+ Open Access articles
OpenAPI	✅ Yes
Auth	Free API key
Rate limit	10 req/sec
Format	JSON
Priority	⭐⭐ Medium

Strengths:

Massive OA aggregator
Full text available
Enriched metadata
Well-documented API

Alpha construction:

bash

# OpenAPI spec available
atlas-openapi-validator fetch \
  https://api.core.ac.uk/docs/v3/openapi.json \
  --output specs/alpha/core-2025-01.yaml \
  --set-stage alpha

Documentation: https://api.core.ac.uk/docs/v3

Paid Sources

Scopus (Elsevier)

Aspect	Detail
URL	`https://api.elsevier.com/`
Operator	Elsevier
Coverage	90M+ records, citations
OpenAPI	✅ Yes
Auth	API key (subscription)
Rate limit	Variable by tier
Format	JSON, XML
Priority	💰 Paid

Strengths:

Very complete citations
h-index, metrics
Exhaustive coverage
Verified affiliations

Alpha construction:

bash

# Requires institutional subscription
# Spec available via dev portal

atlas-openapi-validator fetch \
  https://dev.elsevier.com/api-docs \
  --output specs/alpha/scopus-2025-01.yaml \
  --set-stage alpha \
  --requires-auth

# Tests only with valid credentials

Documentation: https://dev.elsevier.com/documentation/

Web of Science (Clarivate)

Aspect	Detail
URL	`https://api.clarivate.com/apis/wos-starter/`
Operator	Clarivate
Coverage	90M+ records, Impact Factor
OpenAPI	✅ Yes
Auth	API key (subscription)
Rate limit	Variable by tier
Format	JSON
Priority	💰 Paid

Strengths:

Official Impact Factor
Very reliable citations
Historical coverage
Journal rankings

Alpha construction:

bash

# Requires subscription
atlas-openapi-validator fetch \
  https://developer.clarivate.com/apis/wos/swagger \
  --output specs/alpha/wos-2025-01.yaml \
  --set-stage alpha \
  --requires-auth

Documentation: https://developer.clarivate.com/apis/wos

IEEE Xplore

Aspect	Detail
URL	`https://ieeexploreapi.ieee.org/`
Operator	IEEE
Coverage	6M+ engineering articles
OpenAPI	✅ Yes
Auth	API key (subscription)
Rate limit	200 req/day (free), more with subscription
Format	JSON, XML
Priority	💰 Paid (limited free tier)

Strengths:

Reference in engineering/electronics
IEEE standards
Major conferences (CVPR, etc.)

Alpha construction:

bash

# Free tier available (limited)
atlas-openapi-validator fetch \
  https://developer.ieee.org/docs/api \
  --output specs/alpha/ieee-2025-01.yaml \
  --set-stage alpha

Documentation: https://developer.ieee.org/

Dimensions (Digital Science)

Aspect	Detail
URL	`https://app.dimensions.ai/api/`
Operator	Digital Science
Coverage	130M+ publications, grants, patents
OpenAPI	⚠️ DSL API
Auth	API key (subscription)
Rate limit	Variable
Format	JSON
Priority	💰 Paid

Strengths:

Publications-grants-patents links
Integrated Altmetrics
Funding data
Clinical trials

Alpha construction:

bash

# DSL (Domain Specific Language) API, not standard REST
# Requires specific adaptation

atlas-openapi-validator scaffold \
  --name dimensions \
  --base-url https://app.dimensions.ai/api \
  --output specs/alpha/dimensions-2025-01.yaml \
  --notes "DSL-based API, requires special handling"

Documentation: https://docs.dimensions.ai/dsl/

Summary Table

Source	OpenAPI	Free	Priority	Build Method
Semantic Scholar	✅	✅	⭐⭐⭐	Fetch official
PubMed	⚠️	✅	⭐⭐⭐	Doc + inference
Europe PMC	✅	✅	⭐⭐	Fetch + adaptation
Unpaywall	❌	✅	⭐⭐⭐	Doc + inference
OpenCitations	✅	✅	⭐⭐⭐	Fetch official
DataCite	✅	✅	⭐⭐	Fetch (JSON:API)
DOAJ	✅	✅	⭐⭐	Fetch official
Zenodo	✅	✅	⭐⭐	Fetch official
DBLP	❌	✅	⭐⭐	Doc + inference
RePEc	❌	✅	⭐	Manual
bioRxiv	❌	✅	⭐⭐	Doc + inference
CORE	✅	✅	⭐⭐	Fetch official
CiNii	⚠️	✅	⭐	Doc + inference
SciELO	❌	✅	⭐	Solr inference
Scopus	✅	💰	💰	Fetch (auth)
Web of Science	✅	💰	💰	Fetch (auth)
IEEE Xplore	✅	💰	💰	Fetch (auth)
Dimensions	⚠️	💰	💰	DSL specific
SSRN	❌	💰	❌	Not recommended
CNKI	❌	💰	❌	Not recommended

Implementation Recommendation

Phase 1 (Core - already planned)

OpenAlex
Crossref
HAL
ArXiv
ORCID

Phase 2 (Priority extensions)

Semantic Scholar - Spec available, data-rich
Unpaywall - Simple, enriches OA
OpenCitations - Open citation graph

Phase 3 (Specific domains)

PubMed - Essential for biomedicine
bioRxiv/medRxiv - Bio preprints
DBLP - CS reference

Phase 4 (Aggregators)

Europe PMC - PubMed EU complement
CORE - OA full text
DataCite - Research data

Paid sources (optional)

Scopus, WoS, IEEE: according to institutional needs

Bibliographic Sources Catalog ​

Overview ​

Legend ​

Major Academic Sources (Free) ​

Semantic Scholar ​

PubMed / NCBI E-utilities ​

Europe PMC ​

Unpaywall ​

OpenCitations ​

DataCite ​

DOAJ (Directory of Open Access Journals) ​

Zenodo ​

Specialized Sources (Free) ​

DBLP (Computer Science) ​

RePEc (Economics) ​

SSRN (Social Sciences) ​

bioRxiv / medRxiv ​

Regional Sources ​

CNKI (China National Knowledge Infrastructure) ​

CiNii (Japan) ​

SciELO (Latin America) ​

CORE (UK Aggregator) ​

Paid Sources ​

Scopus (Elsevier) ​

Web of Science (Clarivate) ​

IEEE Xplore ​

Dimensions (Digital Science) ​

Summary Table ​

Implementation Recommendation ​

Phase 1 (Core - already planned) ​

Phase 2 (Priority extensions) ​

Phase 3 (Specific domains) ​

Phase 4 (Aggregators) ​

Paid sources (optional) ​

Bibliographic Sources Catalog

Overview

Legend

Major Academic Sources (Free)

Semantic Scholar

PubMed / NCBI E-utilities

Europe PMC

Unpaywall

OpenCitations

DataCite

DOAJ (Directory of Open Access Journals)

Zenodo

Specialized Sources (Free)

DBLP (Computer Science)

RePEc (Economics)

SSRN (Social Sciences)

bioRxiv / medRxiv

Regional Sources

CNKI (China National Knowledge Infrastructure)

CiNii (Japan)

SciELO (Latin America)

CORE (UK Aggregator)

Paid Sources

Scopus (Elsevier)

Web of Science (Clarivate)

IEEE Xplore

Dimensions (Digital Science)

Summary Table

Implementation Recommendation

Phase 1 (Core - already planned)

Phase 2 (Priority extensions)

Phase 3 (Specific domains)

Phase 4 (Aggregators)

Paid sources (optional)