OMIM API


Overview:

The OMIM API URLs are organized in a very simple fashion:

/api/[handler]?[parameters]

/api/[handler]/[component]?[parameters]

/api/[handler]/[action]?[parameters]

The handler refers to the data object, such as an entry or a clinical synopsis.

The component is optional and refers to a specific data component within a data object for example references within an entry.

The action is optional and refers to an action to be performed on a data object, such as a search for entries.

For basic 'GET's, the component or action are usually optional.

The parameters would include things such as MIM numbers, data retrieval options and data formatting options.

Since this is a read-only database, 'GET' is the only HTTP method for public access, all other HTTP methods will return an error (except for the apiKey handle which supports 'POST' and 'DELETE').


Basics:

1.1
1.1
1.4
1.5

Handlers:

2.1
2.3
2.4
2.5
2.6
2.7


1.1
Basic Search

The API key is a key that is unique to every developer wanting to access the API. It is allocated by OMIM and should not be shared. This has to be included with every request and is validated before the request is processed. There are three ways in which it can be included with a request.

Added as an HTTP Header as follows:

ApiKey: nfNEOscLNWWXdSmUoMLPPA

Added as a cookie as follows:

Cookie: ApiKey=nfNEOscLNWWXdSmUoMLPPA

Added as a parameter to the url request as follows:

https://api.omim.org/....?...&apiKey=nfNEOscLNWWXdSmUoMLPPA

Note that the API key parameter name is case-sensitive.


1.2
Generic Parameters

There are a number of generic parameters which are supported by all handler, these being:

Parameter Description
format This specifies the format of the data returned, these include 'html', 'xml', 'json', 'jsonp', 'python' and 'ruby' (for example 'format=xml'). The html format is just the xml with a stylesheet applied to it, this application is done in the API itself. This allows a developer to get responses from the API marked up in html suitable for a web browser. Note that 'text' is only useful in very specific cases.
jsonp/callback This specifies the callback function name for 'jsonp'. If omitted or invalid, the callback function defaults to 'omimWrapper'.
debug This returns debug output of what the API received from the client (for example 'debug=true'). No data will be returned.
style This causes the API to include stylesheet URL for rendering by a browser (for example 'style=true'). This is only useful for the 'xml' format, and allows the client to render the XML into HTML locally as opposed to having the API do it for them.

1.3
API HTML Interface

The API provides a simple, yet powerful, HTML based interface to see how urls are structured.

The home page of the HTML based interface is:

https://api.omim.org/api/html


1.4
Limits

The API will limit how many entries can be retrieved in a single request.

Entries and clinical synopses are limited to 20 per request if any 'includes' are specified, otherwise there is no limit.

Gene map entries are limited to 100 per request.


1.5
API Hosts

The API host is:

api.omim.org


2.1
'entry' Handler

The entry handler supports the following actions/components:

[none]

This is the default case and requires one parameter 'mimNumber' specifying the MIM entry to be retrieved, for example:

https://api.omim.org/api/entry?mimNumber=100100

Multiple MIM numbers can be specified as follows:

https://api.omim.org/api/entry?mimNumber=100100&mimNumber=100200

or as follows:

https://api.omim.org/api/entry?mimNumber=100100,100200

This will return the mim number, the prefix, the status and the titles.

Additional content can be retrieved using the 'include' parameter, the includes are as follows:

Parameter Description
text Includes the text field sections with the entry.
existFlags Include the 'exists' flags with the entry (clinical synopsis, allelic variant, gene map & phenotype map).
allelicVariantList Includes the allelic variant list with the entry.
clinicalSynopsis Include the clinical synopsis with the entry.
seeAlso Includes the 'see also' field with the entry.
referenceList Include the reference list with the entry.
geneMap Include the gene map/phenotype map data with the entry.
externalLinks Include the external links with the entry.
contributors Includes the 'contributors' field with the entry.
creationDate Includes the 'creation date' field with the entry.
editHistory Includes the 'edit history' field with the entry.
dates Include the dates data with the entry.
all Include the above data with the entry.

For example:

https://api.omim.org/api/entry?mimNumber=100100&include=text&include=geneMap

or:

https://api.omim.org/api/entry?mimNumber=100100&include=text,geneMap

By default the 'text' include will return the entire text which can be quite long. You can specify which text section(s) is returned by appending a colon followed by the text section name to 'text', for example

https://api.omim.org/api/entry?mimNumber=100100&include=text:clinicalFeatures

The text sections are:

Section Description
animalModel Animal Model
biochemicalFeatures Biochemical Features
clinicalFeatures Clinical Features
clinicalManagement Clinical Management
cloning Cloning
cytogenetics Cytogenetics
description Description
diagnosis Diagnosis
evolution Evolution
geneFamily Gene Family
geneFunction Gene Function
geneStructure Gene Structure
geneTherapy Gene Therapy
geneticVariability Genetic Variability
genotype Genotype
genotypePhenotypeCorrelations Genotype/Phenotype Correlations
heterogeneity Heterogeneity
history History
inheritance Inheritance
mapping Mapping
molecularGenetics Molecular Genetics
nomenclature Nomenclature
otherFeatures Other Features
pathogenesis Pathogenesis
phenotype Phenotype
populationGenetics Population Genetics
text Text (unfielded text section at the start of the entry)

Finally if all the data was needed, one could just specify:

Parameter Description
all Include all the data with the entry.

For example:

https://api.omim.org/api/entry?mimNumber=100100&include=all

It is strongly recommended that only the data that is needed is retrieved in a request. Retrieving unneeded data means that your request will take longer than it normally would.

There is also an 'exclude' parameter to exclude unwanted sections, for example you might want all the data except for the clinical synopsis:

https://api.omim.org/api/entry?mimNumber=100100&include=all&exclude=clinicalSynopsis

'search'

Searching is provided by SOLR and uses the extended dismax parser:

OMIM Search Help

OMIM Search Fields

Apache SOLR

Apache Lucene

SOLR Help

SOLR Searching Help

This allows the client to perform a search with the following parameters:

Parameter Description
search The search (required)
filter The filter (optional)
fields The fields, defaults to 'number^5 title^3 default'
sort The sort order to use, defaults to 'score desc'
operator The operator to use
start The start offset into the results, default is 0
limit The number of results to return, default is 10
retrieve To retrieve the gene map or clinical synopses corresponding to the entries instead of the entries themselves

For example:

https://api.omim.org/api/entry/search?search=duchenne&start=0&limit=20

Additionally all the parameters listed in the section above also apply, for example:

https://api.omim.org/api/entry/search?search=duchenne&start=0&limit=20&include=geneMap

The 'operator' parameter is optional and can be used to require returned documents to contain all the terms in the search:

Parameter Description
AND to require returned documents to contain all the terms in the search

The 'sort' parameter takes the any of the search fields available in the entry index, some useful sort orders include:

Parameter Description
score desc for descending score order
score desc, prefix_sort desc for descending score order, and descending prefix sort order
date_created desc for descending date created order
date_created asc for ascending date created order
date_updated desc for descending date updated order
date_updated asc for ascending date updated order

For example:

https://api.omim.org/api/entry/search?search=duchenne&sort=score+desc

If unspecified, the sort defaults to 'score desc'. Note that the sort order ('asc' or 'desc') is required.

The 'retrieve' parameter allows the retrieval of the gene map or clinical synopses corresponding to the entries instead of the entries themselves:

Parameter Description
geneMap to retrieve the corresponding gene map
clinicalSynopsis to retrieve the corresponding clinical synopses

Note that search can also be done through the search handler, in this case the handler and the action are flipped, so:

https://api.omim.org/api/entry/search?search=duchenne&start=0&limit=20&include=geneMap

is the same as:

https://api.omim.org/api/search/entry?search=duchenne&start=0&limit=20&include=geneMap

'allelicVariantList'

This allows the client to retrieve the allelic variants for the specified MIM entry, for example:

https://api.omim.org/api/entry/allelicVariantList?mimNumber=100100

'referenceList'

This allows the client to retrieve the references for the specified MIM entry, for example:

https://api.omim.org/api/entry/referenceList?mimNumber=100100


Entry Data:

Field Comments
omim
entryList
entry
prefix
mimNumber
titles
preferredTitle title and symbol, delimited with ';'
includedTitles titles are delimited with ';;', and title/symbols are delimited with ';'
status 'live', 'moved', 'removed'
movedTo Will be set to the target entry mim number if this was moved
clinicalSynopsisExists true|false - depending on whether a clinical synopsis exists, set if the 'exists' include was set
allelicVariantExists true|false - depending on whether an allelic variant exists, set if the 'exists' include was set
geneMapExists true|false - depending on whether a gene map exists, set if the 'exists' include was set
phenotypeMapExists true|false - depending on whether a phenotype map exists, set if the 'exists' include was set
phenotypicSeriesExists true|false - depending on whether a phenotypic series exists, set if the 'exists' include was set
textSectionList text section list in order
textSection
textSectionName
textSectionTitle
textSectionContent
allelicVariantList
allelicVariant
number
status 'live', 'moved', 'removed'
movedTo Will be set to the target entry mim number if this was moved
name
alternativeNames
mutations
text
clinvarAccessions triple semi-colon list of ClinVar accession
dbSnps comma delimited list of dbSNPs
exacDbSnps ExAC dbSNPs
seeAlso see-also list, delimited with ';'
referenceList
reference
mimNumber
referenceNumber
authors
title
source
pubmedID
articleUrl
doi
geneMapList
geneMap
sequenceID
chromosome 1-24
chromosomeSymbol 1-22, X, Y
chromosomeSort
chromosomeLocationStart (if available)
chromosomeLocationEnd (if available)
transcript (if available)
cytoLocation
computedCytoLocation (if available)
mimNumber
geneSymbols Comma delimited list of symbols
geneName
mappingMethod
confidence (deprecated)
references
comments
mouseGeneSymbol
mouseMgiID
geneInheritance
phenotypeMapList
phenotypeMap
mimNumber
phenotype
phenotypeMimNumber
phenotypicSeriesNumber Comma delimited list of phenotypic series numbers
phenotypeMappingKey
phenotypeInheritance
phenotypeMapList
phenotypeMap
mimNumber
phenotype
phenotypeMimNumber
phenotypicSeriesNumber Comma delimited list of phenotypic series numbers
phenotypeMappingKey
phenotypeInheritance
sequence ID Gene map sequence ID
chromosome 1-24
chromosomeSymbol 1-22, X, Y
chromosomeSort
chromosomeLocationStart (if available)
chromosomeLocationEnd (if available)
transcript (if available)
cytoLocation
computedCytoLocation (if available)
geneSymbols Comma delimited list of symbols
geneInheritance
externalLinks
approvedGeneSymbols comma delimited list of approved gene symbols
geneIDs comma delimited list of entrez gene IDs
ncbiReferenceSequences comma delimited list of NCBI reference sequences
genbankNucleotideSequences comma delimited list of genbank nucleotide sequences
proteinSequences comma delimited list of protein sequences
uniGenes comma delimited list of uni genes
ensemblIDs triple-colon delimited list of coma-delimited ensembl ID pairs
swissProtIDs comma delimited list of swiss prot IDs
locusSpecificDBs triple semi-colon delimited database name/url tuples, each tuple is double semi-colon delimited
mgiIDs comma delimited list of MGI IDs
mgiHumanDisease MGI human disease flag (true|false)
wormbaseIDs comma delimited list of wormbase IDs
wormbaseDO wormbase DO
nbkIDs triple semi-colon delimited list of double semi-colon delimited NBK ID/clinical disease name pairs
possumSyndromes triple semi-colon delimited list of double semi-colon delimited possum ID/possum syndrome name pairs
flybaseIDs comma delimited list of flybase IDs
zfinIDs comma delimited list of zfin IDs
newbornScreeningUrls triple semi-colon delimited list of newborn screening urls
hprdIDs comma delimited list of hprd IDs
coriellDiseases triple semi-colon delimited list of double semi-colon delimited coriell disease
dermAtlas DermAtlas entry flag (true|false)
orphanetDiseases triple semi-colon delimited list of double semi-colon delimited orphanet ID/disease pairs
refSeqAccessionIDs !RefSeq accession IDs
ordrDiseases GARD/ORDR diseases
decipherUrls DECIPHER urls
geneticsHomeReferenceIDs Genetics Home Reference IDs
omiaIDs OMIA IDs
snomedctIDs SNOMEDCT IDs
icd10cmIDs ICD10CM IDs
icd9cmIDs ICD9CM IDs
umlsIDs UMLS IDs
gtr GTR
diseaseOntologyIDs Disease Ontology IDs
geneticAllianceIDs Genetic Alliance IDs
cmgGene CMG Gene
keggPathways KEGG Pathways
gwasCatalog GWAS Catalog
clinGen ClinGen
monarch monarch
contributors
creationDate
editHistory
dateCreated Web date
epochCreated Unix epoch
dateUpdated Web date
epochUpdated Unix epoch

Entry Allelic Variant Data:

Field Comments
omim
allelicVariantLists
allelicVariantList
allelicVariant
prefix
mimNumber
preferredTitle
number
status 'live', 'moved', 'removed'
movedTo Will be set to the target entry mim number if this was moved
name
alternativeNames
mutations
text
dbSNPs comma-delimited list of dbSNPs

Entry Reference Data:

Field Comments
omim
referenceLists
referenceList
reference
mimNumber
referenceNumber
authors
title
source
pubmedID
articleUrl
doi

2.2
'clinicalSynopsis' Handler

The clinical synopsis handler supports the following actions/components:

[none]

This is the default case and requires one parameter 'mimNumber' specifying the MIM entry to be retrieved, for example:

https://api.omim.org/api/clinicalSynopsis?mimNumber=100100

Multiple MIM numbers can be specified as follows:

https://api.omim.org/api/clinicalSynopsis?mimNumber=100100&mimNumber=100200

or as follows:

https://api.omim.org/api/clinicalSynopsis?mimNumber=100100,100200

This will return the mim number, the prefix, the status and the titles.

Additional content can be retrieved using the 'include' parameter, the includes are as follows:

Parameter Description
clinicalSynopsis Include the clinical synopsis with the entry.
existFlags Include the 'exists' flags with the entry (clinical synopsis, allelic variant, gene map & phenotype map).
externalLinks Include the external links with the entry.
contributors Include the contributors with the entry.
creationDate Include the creation date with the entry.
editHistory Include the edit history with the entry.
dates Include the dates with the entry.
all Include the above data with the entry.

For example:

https://api.omim.org/api/clinicalSynopsis?mimNumber=100100&include=clinicalSynopsis&include=externalLinks

or:

https://api.omim.org/api/clinicalSynopsis?mimNumber=100100&include=clinicalSynopsis,externalLinks

Finally if all the data was needed, one could just specify:

Parameter Description
all Include all the data with the entry.

For example:

https://api.omim.org/api/clinicalSynopsis?mimNumber=100100&include=all

It is strongly recommended that only the data that is needed is retrieved in a request. Retrieving unneeded data means that your request will take longer than it should.

There is also an 'exclude' parameter to exclude unwanted sections, for example you might want all the data except for the external links:

https://api.omim.org/api/clinicalSynopsis?mimNumber=100100&include=all&exclude=externalLinks

'search'

Searching is provided by SOLR and uses the extended dismax parser:

OMIM Search Help

Clinical Synopsis Search Fields

Apache SOLR

Apache Lucene

SOLR Help

SOLR Searching Help

This allows the client to perform a search with the following parameters:

Parameter Description
search The search (required)
filter The filter (optional)
fields The fields, defaults to 'number^5 title^3 default'
sort The sort order to use, defaults to 'score desc'
start The start offset into the results, default is 0
limit The number of results to return, default is 10

For example:

https://api.omim.org/api/clinicalSynopsis/search?search=disorder&start=0&limit=20

Additionally all the parameters listed in the section above also apply, for example:

https://api.omim.org/api/clinicalSynopsis/search?search=disorder&start=0&limit=20&include=all

The 'sort' parameter takes the any of the search fields available in the clinical synopsis index, some useful sort orders include:

Parameter Description
score desc for descending score order
score desc, prefix_sort desc for descending score order, and descending prefix sort order
date_created desc for descending date created order
date_created asc for ascending date created order
date_updated desc for descending date updated order
date_updated asc for ascending date updated order

For example:

https://api.omim.org/api/clinicalSynopsis/search?search=disorder&sort=score+desc

If unspecified, the sort defaults to 'score desc'. Note that the sort order ('asc' or 'desc') is required.

Note that search can also be done through the search handler, in this case the handler >and the action are flipped, so:

https://api.omim.org/api/clinicalSynopsis/search?search=disorder&start=0&limit=20

is the same as:

https://api.omim.org/api/search/clinicalSynopsis?search=disorder&start=0&limit=20


Clinical Synopsis Data:

Field Comments
omim
clinicalSynopsisList
clinicalSynopsis
mimNumber
prefix
preferredTitle Title taken from the mim entry
inheritance Features in all fields are delimited with ';'
growth and include IDs for UMLS, SNOMEDCT,
growthHeight ICD10CM, ICD9CM and HPO
growthWeight
growthOther
headAndNeck
headAndNeckHead
headAndNeckFace
headAndNeckEars
headAndNeckEyes
headAndNeckNose
headAndNeckMouth
headAndNeckTeeth
headAndNeckNeck
cardiovascular
cardiovascularHeart
cardiovascularVascular
respiratory
respiratoryNasopharynx
respiratoryLarynx
respiratoryAirways
respiratoryLung
chest
chestExternalFeatures
chestRibsSternumClaviclesAndScapulae
chestBreasts
chestDiaphragm
abdomen
abdomenExternalFeatures
abdomenLiver
abdomenPancreas
abdomenBiliaryTract
abdomenSpleen
abdomenGastrointestinal
genitourinary
genitourinaryExternalGenitaliaMale
genitourinaryExternalGenitaliaFemale
genitourinaryInternalGenitaliaMale
genitourinaryInternalGenitaliaFemale
genitourinaryKidneys
genitourinaryUreters
genitourinaryBladder
skeletal
skeletalSkull
skeletalSpine
skeletalPelvis
skeletalLimbs
skeletalHands
skeletalFeet
skinNailsHair
skinNailsHairSkin
skinNailsHairSkinHistology
skinNailsHairSkinElectronMicroscopy
skinNailsHairNails
skinNailsHairHair
muscleSoftTissue
neurologic
neurologicCentralNervousSystem
neurologicPeripheralNervousSystem
neurologicBehavioralPsychiatricManifestations
voice
metabolicFeatures
endocrineFeatures
hematology
immunology
neoplasia
prenatalManifestations
prenatalManifestationsMovement
prenatalManifestationsAmnioticFluid
prenatalManifestationsPlacentaAndUmbilicalCord
prenatalManifestationsMaternal
prenatalManifestationsDelivery
laboratoryAbnormalities
miscellaneous
molecularBasis
inheritanceExists true if this contains data (ii)
growthExists true if this and any its subheadings contain data (i)
growthHeightExists (ii)
growthWeightExists (ii)
growthOtherExists (ii)
headAndNeckExists (i)
headAndNeckHeadExists (ii)
headAndNeckFaceExists (ii)
headAndNeckEarsExists (ii)
headAndNeckEyesExists (ii)
headAndNeckNoseExists (ii)
headAndNeckMouthExists (ii)
headAndNeckTeethExists (ii)
headAndNeckNeckExists (ii)
cardiovascularExists (i)
cardiovascularHeartExists (ii)
cardiovascularVascularExists (ii)
respiratoryExists (i)
respiratoryNasopharynxExists (ii)
respiratoryLarynxExists (ii)
respiratoryAirwaysExists (ii)
respiratoryLungExists (ii)
chestExists (i)
chestExternalFeaturesExists (ii)
chestRibsSternumClaviclesAndScapulaeExists (ii)
chestBreastsExists (ii)
chestDiaphragmExists (ii)
abdomenExists (i)
abdomenExternalFeaturesExists (ii)
abdomenLiverExists (ii)
abdomenPancreasExists (ii)
abdomenBiliaryTractExists (ii)
abdomenSpleenExists (ii)
abdomenGastrointestinalExists (ii)
genitourinaryExists (i)
genitourinaryExternalGenitaliaMaleExists (ii)
genitourinaryExternalGenitaliaFemaleExists (ii)
genitourinaryInternalGenitaliaMaleExists (ii)
genitourinaryInternalGenitaliaFemaleExists (ii)
genitourinaryKidneysExists (ii)
genitourinaryUretersExists (ii)
genitourinaryBladderExists (ii)
skeletalExists (i)
skeletalSkullExists (ii)
skeletalSpineExists (ii)
skeletalPelvisExists (ii)
skeletalLimbsExists (ii)
skeletalHandsExists (ii)
skeletalFeetExists (ii)
skinNailsHairExists (i)
skinNailsHairSkinExists (ii)
skinNailsHairSkinHistologyExists (ii)
skinNailsHairSkinElectronMicroscopyExists (ii)
skinNailsHairNailsExists (ii)
skinNailsHairHairExists (ii)
muscleSoftTissueExists (ii)
neurologicExists (i)
neurologicCentralNervousSystemExists (ii)
neurologicPeripheralNervousSystemExists (ii)
neurologicBehavioralPsychiatricManifestationsExists (ii)
voiceExists (ii)
metabolicFeaturesExists (ii)
endocrineFeaturesExists (ii)
hematologyExists (ii)
immunologyExists (ii)
neoplasiaExists (ii)
prenatalManifestationsExists (i)
prenatalManifestationsMovementExists (ii)
prenatalManifestationsAmnioticFluidExists (ii)
prenatalManifestationsPlacentaAndUmbilicalCordExists (ii)
prenatalManifestationsMaternalExists (ii)
prenatalManifestationsDeliveryExists (ii)
laboratoryAbnormalitiesExists (i)
miscellaneousExists (ii)
molecularBasisExists (ii)
oldFormat Old format clinical synopsis, will be remapped to new format
externalLinks See above for external links
contributors
creationDate
editHistory
dateCreated Web date
epochCreated Unix epoch
dateUpdated Web date
epochUpdated Unix epoch

2.3
'geneMap' Handler

The gene map handler supports the following actions/components:

[none]

This is the default case and supports three different parameters to retrieve data ('chromosomeSort' is a sub-parameter of 'chromosome'):

Parameter Description
sequenceID The sequence ID in the gene map (these are sequential integer values with no breaks and are not stable beyond the scope of a day).
mimNumber The mim number.
chromosome The chromosome, 1-22, 23 (X), 24 (Y), 25 (M), X, Y, M (mitochondria), A (autosomal group), S (XY group)
chromosomeSort The chromosome sort in the chromosome (these are sequential integer values with no breaks and are not stable beyond the scope of a day).

The 'sequenceID' and 'chromosome/chromosomeSort' parameters also support the 'start' and 'limit' parameters to support navigation across the map:

Parameter Description
start The start offset into the gene map, default is 0 (can be negative when getting a list from a sequence ID
limit The number of entries to return, default is 10

Additionally the 'phenotypeExists' flag can be used to restrict the entries returned to those with or without phenotypes, the default is to return all entries:

Parameter Description
Description
phenotypeExists 'true' will only return entries with phenotypes, 'false' will only return entries without phenotypes

For example, to retrieve the gene map entry for 100100:

https://api.omim.org/api/geneMap?mimNumber=100100

Multiple MIM numbers can be specified as follows:

https://api.omim.org/api/geneMap?mimNumber=100100&mimNumber=100200

Or as follows:

https://api.omim.org/api/geneMap?mimNumber=100100,100200

To retrieve the gene map entry for sequence ID 10:

https://api.omim.org/api/geneMap?sequenceID=10

To retrieve the next 10 entries in the gene map starting from sequence ID 10:

https://api.omim.org/api/geneMap?sequenceID=10&limit=10

To get the subsequent 10 entries, the url would be:

https://api.omim.org/api/geneMap?sequenceID=20&limit=10

In the two cases above the 'start' parameter defaults to 0, but you can set to a negative value:

https://api.omim.org/api/geneMap?sequenceID=20&start=-4&limit=10

To retrieve the first 10 entries in the gene map for chromosome 1, the url would be:

https://api.omim.org/api/geneMap?chromosome=1&start=0&limit=10

And to retrieve the next 10 entries, the url would be:

https://api.omim.org/api/geneMap?chromosome=1&start=10&limit=10

The 'chromosomeSort' parameter can also be used to retrieve entries on a chromosome

To retrieve the first 10 entries in the gene map for chromosome 1, the url would be:

https://api.omim.org/api/geneMap?chromosome=1&chromosomeSort=1limit=10

And to retrieve the next 10 entries, the url would be:

https://api.omim.org/api/geneMap?chromosome=1&chromosomeSort=10&limit=10

This can be mixed with 'start' parameter as well:

https://api.omim.org/api/geneMap?chromosome=1&chromosomeSort=1&start=1&limit=10

The 'sequenceID' and 'chromosomeSort' parameters should not be considered stable beyond the scope of a day (the gene map is updated on a daily basis).

'search'

Searching is provided by SOLR and uses the extended dismax parser:

OMIM Search Help

Gene Map Search Fields

Apache SOLR

Apache Lucene

SOLR Help

SOLR Searching Help

This allows the client to perform a search with the following parameters:

Parameter Description
search The search (required)
filter The filter (optional)
fields The fields, defaults to 'default'
sort The sort order to use, defaults to 'score desc'
start The start offset into the results, default is 0
limit The number of results to return, default is 10

For example:

https://api.omim.org/api/geneMap/search?search=kinase&start=0&limit=20

The 'sort' parameter takes the any of the search fields available in the gene map index, some useful sort orders include:

Parameter Description
score desc for descending score order
chromosome_number asc for ascending chromosome number order
chromosome_number asc, chromosome_location_start asc for ascending chromosome number order, and chromosome location start order

If unspecified, the sort defaults to 'score desc'. Note that the sort order ('asc' or 'desc') is required.

Note that search can also be done through the search handler, in this case the handler and the action are flipped, so:

https://api.omim.org/api/geneMap/search?search=kinase&start=0&limit=20

is the same as:

https://api.omim.org/api/search/geneMap?search=kinase&start=0&limit=20


Gene Map Data:

Field Comments
omim
listResponse
chromosome 1-24
chromosomeSymbol 1-22, X, Y
totalResults
startIndex
endIndex
geneMapList
geneMap
sequenceID
chromosome 1-24
chromosomeSymbol 1-22, X, Y
chromosomeSort
chromosomeLocationStart (if available)
chromosomeLocationEnd (if available)
transcript (if available)
cytoLocation
computedCytoLocation (if available)
mimNumber
geneSymbols Comma delimited list of symbols
geneName
mappingMethod
confidence (Deprecated, will be removed October 1st, 2018)
references
comments
mouseGeneSymbol
mouseMgiID
geneInheritance
phenotypeMapList
phenotypeMap
mimNumber
phenotype
phenotypeMimNumber
phenotypicSeriesNumber Comma delimited list of phenotypic series numbers
phenotypeMappingKey
phenotypeInheritance

2.4
'search' Handler

The 'search' handler is used for searching and is covered in the four handlers above.


Search Response Data:

Field Comments
omim
searchResponse
search
expandedSearch
parsedSearch
searchSuggestion
searchSpelling
filter
expandedFilter
fields
searchReport
totalResults
startIndex
endIndex
sort
searchTime
*List List of enty/clinicalSynopsis/geneMap/phenotypeMap

2.5
'html' Handler

The 'html' handler is used to return specific files from the API, and is only useful to the API HTML Interface.

For example:

https://api.omim.org/api/html


2.6
'apiKey' Handler

The apiKey handler allows the API html interface to set an API key in the browser cookies. It supports only one parameter:

Parameter Description
apiKey The api key

For example to set a key in the browser cookies ('POST' method only):

https://api.omim.org/api/apiKey?apiKey=foo

And to remove a key from the browser cookies ('DELETE' method only):

https://api.omim.org/api/apiKey

This is here only to support the API html interface.


2.7
'dump' Handler

The 'dump' handle is used to return dump/debug data from the API.

For example:

https://api.omim.org/api/dump