PubCaseFinder: Search system for rare genetic diseases

OVERVIEW

The PubCaseFinder API uses a fixed URL syntax that translates a standard set of input parameters to return the requested data. In order not to overload the PubCaseFinder servers, DBCLS recommends that users post no more than one URL request per second and limit large jobs to either weekends or between 11:00 PM and 5:00 AM (JST) during weekdays.

API conventions

The PubCaseFinder API currently supports the following functionalities.

RANKED LIST: https://pubcasefinder.dbcls.jp/api/get_ranked_list?target=[RANKED_LIST_TARGET]&format=[RANKED_LIST_FORMAT]&hpo_id=[HPO_ID]
DATA RECORD: https://pubcasefinder.dbcls.jp/api/get_data_record?target=[RECORD_TARGET]&id=[RECORD_ID]
DISEASE-PHENOTYPE ASSOCIATION: https://pubcasefinder.dbcls.jp/api/get_dpa?target=[DISEASE_TARGET]&id=[DISEASE_ID]
GENE-PHENOTYPE ASSOCIATION: https://pubcasefinder.dbcls.jp/api/get_gpa?id=[GENE_ID]
CASE REPORT: https://pubcasefinder.dbcls.jp/api/get_case_report?id=[MONDO_ID]

RANKED LIST

Any ranked lists can be obtained by indicating the [RANKED_LIST_TARGET], [RANKED_LIST_FORMAT], and [HPO_ID].

URL syntax

https://pubcasefinder.dbcls.jp/api/get_ranked_list?target=[RANKED_LIST_TARGET]&format=[RANKED_LIST_FORMAT]&hpo_id=[HPO_ID]

Parameters

target: "omim" or "orphanet" or "gene"
format: "json" or "tsv"
hpo_id: HPO IDs with commas

Example

A ranked list of genetic diseases (OMIM) using the HPO IDs “HP:0002089” and “HP:0001998” in JavaScript Object Notation (JSON) format can be obtained using the following:
https://pubcasefinder.dbcls.jp/api/get_ranked_list?target=omim&format=json&hpo_id=HP:0002089,HP:0001998

[
    {
        "omim_url": "http://identifiers.org/mim/231680",
        "omim_disease_name_en": "multiple acyl-CoA dehydrogenase deficiency",
        "omim_disease_name_ja": "\u591a\u767a\u6027\u30a2\u30b7\u30eb-CoA \u8131\u6c34\u7d20\u6b20\u4e4f\u75c7 (MADD)",
        "description": "A disorder of fatty acid and amino acid oxidation, caused by mutations in ETFDH, ETFA, or ETFB, and is a clinically heterogeneous disorder ranging from a severe neonatal presentation with metabolic acidosis, cardiomyopathy and liver disease, to a mild childhood/adult disease with episodic metabolic decompensation, muscle weakness, and respiratory failure.",
        "ur_dbms_url": "http://syndromefinder.ncchd.go.jp/UR-DBMS/SyndromeDetail.php?recid=2269&winid=1",
        "count_hpo_id": "32",
        "ncbi_gene_id": [
            "GENEID:2108",
            "GENEID:2109",
            "GENEID:2110"
        ],
        "hgnc_gene_symbol": [
            "ETFA",
            "ETFB",
            "ETFDH"
        ],
        "inheritance_en": {
            "HP:0000007": "Autosomal recessive inheritance"
        },
        "inheritance_ja": {
            "HP:0000007": "\u5e38\u67d3\u8272\u4f53\u52a3\u6027\u907a\u4f1d"
        },
        "mondo_id": [
            "MONDO:0009282"
        ],
        "mondo_url": [
            "https://monarchinitiative.org/disease/MONDO:0009282"
        ],
        "gene_reviews_url": [
            "https://www.ncbi.nlm.nih.gov/books/NBK558236/"
        ],
        "gtr_url": [
            "https://www.ncbi.nlm.nih.gov/gtr/all/tests/?term=C0268596/"
        ],
        "id": "OMIM:231680",
        "rank": 1,
        "score": 0.7940279980972564,
        "matched_hpo_id": "HP:0002089,HP:0001943"
    },
    …
]

DATA RECORD

Each data record in ranked lists of PubCaseFinder can be obtained by indicating the [RECORD_TARGET] and [RECORD_ID].

URL syntax

https://pubcasefinder.dbcls.jp/api/get_data_record?target=[RECORD_TARGET]&id=[RECORD_ID]

Parameters

target: "omim" or "orphanet" or "gene"
id: OMIM ID or ORPHA ID or NCBI Gene ID

Example

A data record for OMIM ID "612690" can be obtained using the following:
https://pubcasefinder.dbcls.jp/api/get_data_record?target=omim&id=612690

{
  "OMIM:612690": {
    "count_hpo_id": "8", 
    "description": "Any hereditary spherocytosis in which the cause of the disease is a mutation in the EPB42 gene.", 
    "gene_reviews_url": [
      "https://www.ncbi.nlm.nih.gov/books/NBK190102/"
    ], 
    "gtr_url": [
      "https://www.ncbi.nlm.nih.gov/gtr/all/tests/?term=C2675192/"
    ], 
    "hgnc_gene_symbol": [
      "EPB42"
    ], 
    "inheritance_en": {
      "HP:0000007": "Autosomal recessive inheritance"
    }, 
    "inheritance_ja": {
      "HP:0000007": "常染色体劣性遺伝"
    }, 
    "mondo_id": [
      "MONDO:0012985"
    ], 
    "mondo_url": [
      "https://monarchinitiative.org/disease/MONDO:0012985"
    ], 
    "ncbi_gene_id": [
      "GENEID:2038"
    ], 
    "omim_disease_name_en": "hereditary spherocytosis type 5", 
    "omim_disease_name_ja": "球状赤血球症5型", 
    "omim_url": "http://identifiers.org/mim/612690", 
    "ur_dbms_url": "http://syndromefinder.ncchd.go.jp/UR-DBMS/SyndromeDetail.php?recid=7206&winid=1"
  }
}

DISEASE-PHENOTYPE ASSOCIATION

Disease-Phenotype associations for each disease in OMIM and Orphanet can be obtained by indicating the [DISEASE_TARGET] and [DISEASE_ID].

URL syntax

https://pubcasefinder.dbcls.jp/api/get_dpa?target=[DISEASE_TARGET]&id=[DISEASE_ID]

Parameters

target: "omim" or "orphanet"
id: OMIM ID or ORPHA ID

Example

Disease-Phenotype associations for the OMIM ID "612690" can be obtained using the following:
https://pubcasefinder.dbcls.jp/api/get_dpa?target=omim&id=612690

[
  {
    "definition": "Yellow pigmentation of the skin due to bilirubin, which in turn is the result of increased bilirubin concentration in the bloodstream.", 
    "hpo_category_name_en": "Abnormality of the integument", 
    "hpo_category_name_ja": "外皮の異常", 
    "hpo_id": "HP:0000952", 
    "hpo_label_en": "Jaundice", 
    "hpo_label_ja": "黄疸", 
    "hpo_url": "http://purl.obolibrary.org/obo/HP_0000952"
  }, 
  …
  {
    "definition": "Abnormal increased size of the spleen.", 
    "hpo_category_name_en": "Abnormality of the digestive system", 
    "hpo_category_name_ja": "消化器系の異常", 
    "hpo_id": "HP:0001744", 
    "hpo_label_en": "Splenomegaly", 
    "hpo_label_ja": "脾腫", 
    "hpo_url": "http://purl.obolibrary.org/obo/HP_0001744"
  }
]

GENE-PHENOTYPE ASSOCIATION

Gene-Phenotype associations for each gene can be obtained by indicating the [GENE_ID].

URL syntax

https://pubcasefinder.dbcls.jp/api/get_gpa?id=[GENE_ID]

Parameters

id: NCBI Gene ID

Example

Gene-Phenotype associations for the NCBI Gene ID "1723" can be obtained using the following:
https://pubcasefinder.dbcls.jp/api/get_gpa?id=1723

[
  {
    "disease": "OMIM", 
    "disease_id": "263750", 
    "hpo_category_name_en": "Abnormality of the genitourinary system", 
    "hpo_category_name_ja": "泌尿生殖器異常", 
    "hpo_id": "HP:0000028", 
    "hpo_label_en": "Cryptorchidism", 
    "hpo_label_ja": "停留精巣", 
    "hpo_url": "http://purl.obolibrary.org/obo/HP_0000028"
  }, 
  …
  {
    "disease": "OMIM", 
    "disease_id": "263750", 
    "hpo_category_name_en": "Abnormality of limbs", 
    "hpo_category_name_ja": "四肢の異常", 
    "hpo_id": "HP:0009778", 
    "hpo_label_en": "Short thumb", 
    "hpo_label_ja": "短い母指", 
    "hpo_url": "http://purl.obolibrary.org/obo/HP_0009778"
  }
]

CASE REPORT

Case reports related to rare genetic diseases in PubMed can be obtained by indicating the [MONDO_ID].

This API can be used for non-commercial purposes only.

URL syntax

https://pubcasefinder.dbcls.jp/api/get_case_report?id=[MONDO_ID]

Parameters

id: Mondo ID

Example

Case reports for the Mondo ID "0008752" can be obtained using the following:
https://pubcasefinder.dbcls.jp/api/get_case_report?id=MONDO:0008752

[
  {
    "id": 30755773, 
    "journal": "Case Rep Med", 
    "pyear": 2019, 
    "title": "A Novel Mutation in the Adult-Onset Alexander's Disease GFAP Gene.", 
    "url": "https://pubmed.ncbi.nlm.nih.gov/30755773"
  }, 
  …
  {
    "id": 180453, 
    "journal": "Neurology", 
    "pyear": 1976, 
    "title": "Alexander's disease: a report and reappraisal.", 
    "url": "https://pubmed.ncbi.nlm.nih.gov/180453"
  }
]