External services
Edifix integrates with three external reference databases to validate, correct, and link references:
- PubMed: Links references to PubMed records (PMIDs and URLs) and can correct reference metadata against PubMed's record.
- Crossref: Adds DOIs and canonical metadata to references, including Crossmark retraction and correction notices.
- Retraction Watch: Flags references to retracted publications.
Per-job flags
The behaviour of each integration is controlled by flags on POST /create_job and POST /create_job_from_file. See the API reference for the full request schema.
| Flag | Effect |
|---|---|
pubmed_flag | When true, Edifix links references to PubMed, and (in the default mode) corrects reference metadata to match PubMed's record. |
crossref_flag | When true, Edifix links references to Crossref, adds DOIs, and includes Crossmark retraction and correction notices. |
book_processing_flag | When true, Edifix processes book references in addition to journal references. |
remove_line_breaks_flag | When true, Edifix removes line breaks inside reference text before parsing. |
WARNING
Retraction Watch runs on every job with no per-job flag. Matches appear as warnings in the output.
Result counts
You can find the per-service result counts in the extended job-info response (see JobInfoExtended in the API reference):
pubmed_linked_refs: References successfully linked to a PubMed record.crossref_linked_refs: References successfully linked to Crossref.retracted_refs: References flagged as retracted by Retraction Watch. Crossmark retraction notices appear as warnings in the reference output but are not counted here.
Service health and failure handling
The GET /get_api_status endpoint reports the current status of each upstream integration. Its response (see ApiStatusResponse in the API reference) is the source of truth for whether each external service is reachable, and includes a reference_service_status field summarising overall integration health.
When PubMed or Crossref is unreachable, Edifix sets the billable reference count to zero so you aren't charged for jobs whose reference linking could not complete. See Error codes for relevant codes, including 0001 (server-side processing error) and 0002 (job timeout).
If Retraction Watch has a service disruption, jobs still complete, but the output will not include warnings for references that could not be checked.