BiomedCore

BiomedCore provides access to 39M+ biomedical citations sourced from PubMed and PubMed Central (PMC), enriched with citation counts, journal quality indicators, and structured metadata. Updated daily.

Endpoints

Search — `GET /v1/cores/biomedcore/records`

Search across biomedical literature by text, with optional filters.

Shell

curl "https://api.amass.tech/api/v1/cores/biomedcore/records?query=CAR-T+therapy&limit=5" \
  -H "Authorization: Bearer amass_YOUR_KEY"

Parameters:

Name	Required	Default	Description
`query`	yes	—	Search text (titles, abstracts, fulltext, metadata)
`limit`	no	20	Results to return (1–300)
`include`	no	—	Optional fields to return. Repeat for multiple: `fulltext`, `authorsMetadata`, `meshIds`, `substanceIds`, `referencesTrialCore`, `references`, `citedBy`
`minPublicationDate`	no	—	ISO date, e.g. `2023-01-01`
`maxPublicationDate`	no	—	ISO date, e.g. `2026-01-01`
`minCitationCount`	no	—	Integer (0–100,000)
`minJournalQualityJufo`	no	—	`0`, `1`, `2`, or `3` (see Journal Quality Tiers)
`isRetracted`	no	—	`true` or `false`
`authorOrcids`	no	—	Match ANY of these ORCIDs. Accepts bare (`0000-0003-1234-5678`) or URL form (`https://orcid.org/0000-0003-1234-5678`). Repeat the param for multiple values. See Author & institution filters.
`authorNames`	no	—	Match ANY of these author names. Free-text token match (no prefix expansion). Repeat the param for multiple values.
`institutionRors`	no	—	Match ANY of these ROR identifiers. Accepts bare (`03vek6s52`) or URL form (`https://ror.org/03vek6s52`). Repeat the param for multiple values.
`institutionNames`	no	—	Match ANY of these institution names. Free-text token match. Repeat the param for multiple values.

Example with filters — highly cited papers in top journals from 2022 onward:

Shell

curl "https://api.amass.tech/api/v1/cores/biomedcore/records\
?query=immunotherapy\
&minPublicationDate=2022-01-01\
&minCitationCount=30\
&minJournalQualityJufo=2" \
  -H "Authorization: Bearer amass_YOUR_KEY"

Author & institution filters

The four filters authorOrcids, authorNames, institutionRors, and institutionNames follow the same encoding and combine with the same rules.

Within one filter — OR. Repeat the param to match any of the listed values: ?authorOrcids=0000-0001-...&authorOrcids=0000-0002-... returns papers authored by either ORCID.
Across filters — AND. Mixing different filters narrows the result: ?authorNames=Hassabis&institutionNames=DeepMind returns papers that have a Hassabis author and a DeepMind affiliation (not necessarily the same author/affiliation pair).
ORCIDs and RORs accept bare or URL form. 0000-0002-2401-5691 and https://orcid.org/0000-0002-2401-5691 match the same author; 03vek6s52 and https://ror.org/03vek6s52 match the same institution.
Author/institution name matching is free-text token. Use the most distinctive token (last name, institution head noun) and combine with query for context. PubMed indexes author names as LastName Initials (e.g. Liu DR), so a last-name token is usually the safest match.

Shell

# Papers by one of two ORCIDs at a specific institution (ROR), since 2022
curl "https://api.amass.tech/api/v1/cores/biomedcore/records\
?query=protein+structure+prediction\
&authorOrcids=0000-0002-2401-5691\
&authorOrcids=0000-0001-9282-0298\
&institutionRors=00971b260\
&minPublicationDate=2022-01-01\
&include=authorsMetadata\
&limit=20" \
  -H "Authorization: Bearer amass_YOUR_KEY"

Response:

JSON

{ "data": [ { "amassId": "AMBC_...", "title": "...", "..." }, ... ] }

Get by ID — `GET /v1/cores/biomedcore/records/{amassId}`

Fetch a single record by its Amass ID.

Shell

curl "https://api.amass.tech/api/v1/cores/biomedcore/records/AMBC_abc123\
?include=authorsMetadata" \
  -H "Authorization: Bearer amass_YOUR_KEY"

Response:

JSON

{ "data": { "amassId": "AMBC_...", "title": "...", "..." } }

Returns 404 if not found.

Lookup — `POST /v1/cores/biomedcore/records/lookup`

Convert PMIDs or DOIs to Amass IDs in batch. Each item must contain exactly one identifier — either pmid or doi, not both.

Shell

curl -X POST "https://api.amass.tech/api/v1/cores/biomedcore/records/lookup" \
  -H "Authorization: Bearer amass_YOUR_KEY" \
  -H "Content-Type: application/json" \
  -d '{
    "items": [
      { "pmid": "38123456" },
      { "doi": "10.1038/s41586-024-00001-x" }
    ]
  }'

Response:

JSON

{
  "data": [
    {
      "input": { "pmid": "38123456" },
      "amassIds": ["AMBC_abc123"]
    },
    {
      "input": { "doi": "10.1038/s41586-024-00001-x" },
      "error": { "code": "NOT_FOUND", "message": "No matching record found" }
    }
  ]
}

Individual items can fail without failing the whole request. Always check each item for an error field.

Record Schema

Default fields (always returned)

Field	Type	Description
`amassId`	string	Unique Amass identifier (`AMBC_...`)
`pmid`	string \| null	PubMed ID
`pmcid`	string \| null	PubMed Central ID
`doi`	string \| null	Digital Object Identifier
`title`	string \| null	Article title
`abstract`	string \| null	Article abstract
`authors`	string[]	Author names (e.g. `["Smith J", "Doe A"]`)
`journal`	string \| null	Journal name
`issn`	string \| null	Journal ISSN
`volumeIssue`	string \| null	Volume and issue
`publicationDate`	string \| null	ISO date
`publicationTypes`	string[]	E.g. `["Journal Article", "Review"]`
`language`	string \| null	Language code (e.g. `eng`)
`citationCount`	number \| null	Citation count
`journalQualityJufo`	number \| null	JuFo journal quality level (0–3, see below)
`meshTerms`	string[]	MeSH terms
`keywords`	string[]	Author keywords
`substances`	string[]	Chemical substances
`hasFulltext`	boolean \| null	Whether full text is available
`isRetracted`	boolean \| null	Whether article is retracted

Optional fields

Request these with the include parameter. Repeat for multiple: ?include=fulltext&include=authorsMetadata

Field	Include value	Type	Description
`fulltext`	`fulltext`	string \| null	Full article text. Large — only request when needed.
`authorsMetadata`	`authorsMetadata`	object[]	Structured author details (see below)
`meshIds`	`meshIds`	string[]	MeSH descriptor identifiers
`substanceIds`	`substanceIds`	string[]	Chemical substance identifiers
`referencesTrialCore`	`referencesTrialCore`	string[]	Cross-core link → TrialCore. Amass IDs of TrialCore records (clinical trials) referenced by this publication
`references`	`references`	string[]	Intra-core link within BiomedCore. Amass IDs of other BiomedCore records (publications) referenced by this publication
`citedBy`	`citedBy`	string[]	Intra-core link within BiomedCore. Amass IDs of other BiomedCore records (publications) that cite this publication

Reference field semantics

╔══════════════════ BiomedCore (publications) ══════════════════╗
║                                                                ║
║   AMBC_aaa ─cites─┐                       ┌─► AMBC_p001        ║
║                   │                       ├─► AMBC_p002        ║
║                   │                       ├─► AMBC_p003        ║
║                   │   ┌──────────┐        │                    ║
║                   ├──►│  AMBC_X  │────────┤        ⋮           ║
║                   │   └──────────┘        │                    ║
║                   │                       ├─► AMBC_p050        ║
║                   │                       ├─► AMBC_p051        ║
║   AMBC_bbb ─cites─┘                       └─► AMBC_p052        ║
║                                                                ║
║   AMBC_X.citedBy    = [AMBC_aaa, AMBC_bbb]           ← 2 IDs   ║
║   AMBC_X.references = [AMBC_p001, …, AMBC_p052]      ← 52 IDs  ║
║                                                                ║
║         ── intra-core: arrows stay within BiomedCore ──        ║
║                                                                ║
╚════════════════════════════════════════════════════════════════╝
                                │
                                │   AMBC_X.referencesTrialCore = [AMTC_xxx]
                                │   ── cross-core link to TrialCore ──
                                ▼
╔══════════════════ TrialCore (clinical trials) ════════════════╗
║                                                                ║
║                           AMTC_xxx                             ║
║                                                                ║
╚════════════════════════════════════════════════════════════════╝

Intra-core arrows stay inside BiomedCore — target IDs start with AMBC_. Both fan-in (citedBy) and fan-out (references) live in the same Core.
Cross-core arrow leaves BiomedCore for TrialCore — target IDs start with AMTC_. Only referencesTrialCore crosses the Core boundary.

`authorsMetadata` shape

JSON

{
  "name": "Smith J",
  "nameRaw": "John Smith",
  "orcid": "0000-0001-2345-6789",
  "position": 0,
  "affiliations": [
    {
      "name": "Harvard Medical School",
      "nameRaw": "Harvard Medical School, Boston, MA, USA",
      "ror": "03vek6s52",
      "countryCode": "US"
    }
  ]
}

Journal Quality Tiers

Journal quality is based on Publication Forum (JuFo), an openly published classification of publication channels.

Level	Meaning
3	Highest quality — represents the highest level in the discipline with extremely consistent impact
2	Domain leading — limited number of journals, conferences, and publishers of the highest level
1	Peer reviewed — peer-reviewed channels specialised in scientific research with an expert editorial board
0	Low quality — evaluated but does not meet all Level 1 criteria
null	Not evaluated — publication channel has not been evaluated

BiomedCore

Endpoints

Search — `GET /v1/cores/biomedcore/records`

Search across biomedical literature by text, with optional filters.

Shell

curl "https://api.amass.tech/api/v1/cores/biomedcore/records?query=CAR-T+therapy&limit=5" \
  -H "Authorization: Bearer amass_YOUR_KEY"

Parameters:

Name	Required	Default	Description
`query`	yes	—	Search text (titles, abstracts, fulltext, metadata)
`limit`	no	20	Results to return (1–300)
`include`	no	—	Optional fields to return. Repeat for multiple: `fulltext`, `authorsMetadata`, `meshIds`, `substanceIds`, `referencesTrialCore`, `references`, `citedBy`
`minPublicationDate`	no	—	ISO date, e.g. `2023-01-01`
`maxPublicationDate`	no	—	ISO date, e.g. `2026-01-01`
`minCitationCount`	no	—	Integer (0–100,000)
`minJournalQualityJufo`	no	—	`0`, `1`, `2`, or `3` (see Journal Quality Tiers)
`isRetracted`	no	—	`true` or `false`
`authorOrcids`	no	—	Match ANY of these ORCIDs. Accepts bare (`0000-0003-1234-5678`) or URL form (`https://orcid.org/0000-0003-1234-5678`). Repeat the param for multiple values. See Author & institution filters.
`authorNames`	no	—	Match ANY of these author names. Free-text token match (no prefix expansion). Repeat the param for multiple values.
`institutionRors`	no	—	Match ANY of these ROR identifiers. Accepts bare (`03vek6s52`) or URL form (`https://ror.org/03vek6s52`). Repeat the param for multiple values.
`institutionNames`	no	—	Match ANY of these institution names. Free-text token match. Repeat the param for multiple values.

Example with filters — highly cited papers in top journals from 2022 onward:

Shell

curl "https://api.amass.tech/api/v1/cores/biomedcore/records\
?query=immunotherapy\
&minPublicationDate=2022-01-01\
&minCitationCount=30\
&minJournalQualityJufo=2" \
  -H "Authorization: Bearer amass_YOUR_KEY"

Author & institution filters

The four filters authorOrcids, authorNames, institutionRors, and institutionNames follow the same encoding and combine with the same rules.

Within one filter — OR. Repeat the param to match any of the listed values: ?authorOrcids=0000-0001-...&authorOrcids=0000-0002-... returns papers authored by either ORCID.
Across filters — AND. Mixing different filters narrows the result: ?authorNames=Hassabis&institutionNames=DeepMind returns papers that have a Hassabis author and a DeepMind affiliation (not necessarily the same author/affiliation pair).
ORCIDs and RORs accept bare or URL form. 0000-0002-2401-5691 and https://orcid.org/0000-0002-2401-5691 match the same author; 03vek6s52 and https://ror.org/03vek6s52 match the same institution.
Author/institution name matching is free-text token. Use the most distinctive token (last name, institution head noun) and combine with query for context. PubMed indexes author names as LastName Initials (e.g. Liu DR), so a last-name token is usually the safest match.

Shell

# Papers by one of two ORCIDs at a specific institution (ROR), since 2022
curl "https://api.amass.tech/api/v1/cores/biomedcore/records\
?query=protein+structure+prediction\
&authorOrcids=0000-0002-2401-5691\
&authorOrcids=0000-0001-9282-0298\
&institutionRors=00971b260\
&minPublicationDate=2022-01-01\
&include=authorsMetadata\
&limit=20" \
  -H "Authorization: Bearer amass_YOUR_KEY"

Response:

JSON

{ "data": [ { "amassId": "AMBC_...", "title": "...", "..." }, ... ] }

Get by ID — `GET /v1/cores/biomedcore/records/{amassId}`

Fetch a single record by its Amass ID.

Shell

curl "https://api.amass.tech/api/v1/cores/biomedcore/records/AMBC_abc123\
?include=authorsMetadata" \
  -H "Authorization: Bearer amass_YOUR_KEY"

Response:

JSON

{ "data": { "amassId": "AMBC_...", "title": "...", "..." } }

Returns 404 if not found.

Lookup — `POST /v1/cores/biomedcore/records/lookup`

Convert PMIDs or DOIs to Amass IDs in batch. Each item must contain exactly one identifier — either pmid or doi, not both.

Shell

curl -X POST "https://api.amass.tech/api/v1/cores/biomedcore/records/lookup" \
  -H "Authorization: Bearer amass_YOUR_KEY" \
  -H "Content-Type: application/json" \
  -d '{
    "items": [
      { "pmid": "38123456" },
      { "doi": "10.1038/s41586-024-00001-x" }
    ]
  }'

Response:

JSON

{
  "data": [
    {
      "input": { "pmid": "38123456" },
      "amassIds": ["AMBC_abc123"]
    },
    {
      "input": { "doi": "10.1038/s41586-024-00001-x" },
      "error": { "code": "NOT_FOUND", "message": "No matching record found" }
    }
  ]
}

Individual items can fail without failing the whole request. Always check each item for an error field.

Record Schema

Default fields (always returned)

Field	Type	Description
`amassId`	string	Unique Amass identifier (`AMBC_...`)
`pmid`	string \| null	PubMed ID
`pmcid`	string \| null	PubMed Central ID
`doi`	string \| null	Digital Object Identifier
`title`	string \| null	Article title
`abstract`	string \| null	Article abstract
`authors`	string[]	Author names (e.g. `["Smith J", "Doe A"]`)
`journal`	string \| null	Journal name
`issn`	string \| null	Journal ISSN
`volumeIssue`	string \| null	Volume and issue
`publicationDate`	string \| null	ISO date
`publicationTypes`	string[]	E.g. `["Journal Article", "Review"]`
`language`	string \| null	Language code (e.g. `eng`)
`citationCount`	number \| null	Citation count
`journalQualityJufo`	number \| null	JuFo journal quality level (0–3, see below)
`meshTerms`	string[]	MeSH terms
`keywords`	string[]	Author keywords
`substances`	string[]	Chemical substances
`hasFulltext`	boolean \| null	Whether full text is available
`isRetracted`	boolean \| null	Whether article is retracted

Optional fields

Request these with the include parameter. Repeat for multiple: ?include=fulltext&include=authorsMetadata

Field	Include value	Type	Description
`fulltext`	`fulltext`	string \| null	Full article text. Large — only request when needed.
`authorsMetadata`	`authorsMetadata`	object[]	Structured author details (see below)
`meshIds`	`meshIds`	string[]	MeSH descriptor identifiers
`substanceIds`	`substanceIds`	string[]	Chemical substance identifiers
`referencesTrialCore`	`referencesTrialCore`	string[]	Cross-core link → TrialCore. Amass IDs of TrialCore records (clinical trials) referenced by this publication
`references`	`references`	string[]	Intra-core link within BiomedCore. Amass IDs of other BiomedCore records (publications) referenced by this publication
`citedBy`	`citedBy`	string[]	Intra-core link within BiomedCore. Amass IDs of other BiomedCore records (publications) that cite this publication

Reference field semantics

╔══════════════════ BiomedCore (publications) ══════════════════╗
║                                                                ║
║   AMBC_aaa ─cites─┐                       ┌─► AMBC_p001        ║
║                   │                       ├─► AMBC_p002        ║
║                   │                       ├─► AMBC_p003        ║
║                   │   ┌──────────┐        │                    ║
║                   ├──►│  AMBC_X  │────────┤        ⋮           ║
║                   │   └──────────┘        │                    ║
║                   │                       ├─► AMBC_p050        ║
║                   │                       ├─► AMBC_p051        ║
║   AMBC_bbb ─cites─┘                       └─► AMBC_p052        ║
║                                                                ║
║   AMBC_X.citedBy    = [AMBC_aaa, AMBC_bbb]           ← 2 IDs   ║
║   AMBC_X.references = [AMBC_p001, …, AMBC_p052]      ← 52 IDs  ║
║                                                                ║
║         ── intra-core: arrows stay within BiomedCore ──        ║
║                                                                ║
╚════════════════════════════════════════════════════════════════╝
                                │
                                │   AMBC_X.referencesTrialCore = [AMTC_xxx]
                                │   ── cross-core link to TrialCore ──
                                ▼
╔══════════════════ TrialCore (clinical trials) ════════════════╗
║                                                                ║
║                           AMTC_xxx                             ║
║                                                                ║
╚════════════════════════════════════════════════════════════════╝

Intra-core arrows stay inside BiomedCore — target IDs start with AMBC_. Both fan-in (citedBy) and fan-out (references) live in the same Core.
Cross-core arrow leaves BiomedCore for TrialCore — target IDs start with AMTC_. Only referencesTrialCore crosses the Core boundary.

`authorsMetadata` shape

JSON

{
  "name": "Smith J",
  "nameRaw": "John Smith",
  "orcid": "0000-0001-2345-6789",
  "position": 0,
  "affiliations": [
    {
      "name": "Harvard Medical School",
      "nameRaw": "Harvard Medical School, Boston, MA, USA",
      "ror": "03vek6s52",
      "countryCode": "US"
    }
  ]
}

Journal Quality Tiers

Journal quality is based on Publication Forum (JuFo), an openly published classification of publication channels.

Level	Meaning
3	Highest quality — represents the highest level in the discipline with extremely consistent impact
2	Domain leading — limited number of journals, conferences, and publishers of the highest level
1	Peer reviewed — peer-reviewed channels specialised in scientific research with an expert editorial board
0	Low quality — evaluated but does not meet all Level 1 criteria
null	Not evaluated — publication channel has not been evaluated

BiomedCore

Endpoints

Search — `GET /v1/cores/biomedcore/records`

Author & institution filters

Get by ID — `GET /v1/cores/biomedcore/records/{amassId}`

Lookup — `POST /v1/cores/biomedcore/records/lookup`

Record Schema

Default fields (always returned)

Optional fields

Reference field semantics

`authorsMetadata` shape

Journal Quality Tiers

See Also

BiomedCore

Endpoints

Search — `GET /v1/cores/biomedcore/records`

Author & institution filters

Get by ID — `GET /v1/cores/biomedcore/records/{amassId}`

Lookup — `POST /v1/cores/biomedcore/records/lookup`

Record Schema

Default fields (always returned)

Optional fields

Reference field semantics

`authorsMetadata` shape

Journal Quality Tiers

See Also

BiomedCore

Endpoints

Search — GET /v1/cores/biomedcore/records

Author & institution filters

Get by ID — GET /v1/cores/biomedcore/records/{amassId}

Lookup — POST /v1/cores/biomedcore/records/lookup

Record Schema

Default fields (always returned)

Optional fields

Reference field semantics

authorsMetadata shape

Journal Quality Tiers

See Also

BiomedCore

Endpoints

Search — GET /v1/cores/biomedcore/records

Author & institution filters

Get by ID — GET /v1/cores/biomedcore/records/{amassId}

Lookup — POST /v1/cores/biomedcore/records/lookup

Record Schema

Default fields (always returned)

Optional fields

Reference field semantics

authorsMetadata shape

Journal Quality Tiers

See Also

Search — `GET /v1/cores/biomedcore/records`

Get by ID — `GET /v1/cores/biomedcore/records/{amassId}`

Lookup — `POST /v1/cores/biomedcore/records/lookup`

`authorsMetadata` shape

Search — `GET /v1/cores/biomedcore/records`

Get by ID — `GET /v1/cores/biomedcore/records/{amassId}`

Lookup — `POST /v1/cores/biomedcore/records/lookup`

`authorsMetadata` shape