OMIM API Help

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 handler which supports 'POST' and 'DELETE' to add/remove the apiKey from the cookies).

Basics:

1.1

API Key

1.2

Generic Parameters

1.3

API HTML Interface

1.4

Limits

1.5

Compression

1.6

API Hosts

1.7

HTTP Status Codes

Handlers:

2.1

entry

2.2

clinicalSynopsis

2.3

geneMap

2.4

2.5

status

2.6

apiKey

1.1

API Key

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 'json' and 'xml' (for example 'format=json').

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.

Results can be retrieved in batches using the 'start' and 'limit' parameters as follows:

...start=0&limit;=20... ...start=20&limit;=20.. ...start=40&limit;=20..

1.5

Compression

The API supports gzip compression so, if possible, you should enable gzip compression in your client to reduce network traffic. Compression can reduce the size of responses by a factor of 4 or 5 which is advantageous in bandwidth-constrained environments.

Compression is automatically supported in some clients, whereas it needs to be specifically enabled in others. Please check the documentation for the client you are using.

The HTTP header indicating that your client can receive a compressed response is as follows:

Accept-Encoding: gzip

For example curl does not enable gzip compression by default, so this will receive an uncompressed response:

curl "https://api.omim.org/api/..."

Adding the HTTP header to will receive a compressed response:

curl -H "Accept-Encoding: gzip" "https://api.omim.org/api/..." | gunzip

1.6

API Hosts

The API host is:

api.omim.org

1.7

HTTP Status Codes

The API returns the following HTTP status codes:

Status	Name	Description
200	OK	The request was successful
400	Bad Request	The request failed because the URL was incorrect
401	Unauthorized	The request failed because the API key is invalid or inactive
404	Not Found	The request failed because the data requested does not exist
429	Too Many Requests	The request failed because the quota for the API key has been exceeded
500	Internal Server Error	The request failed because of an internal server error

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 Name	Section Title
animalModel	Animal Model
biochemicalFeatures	Biochemical Features
clinicalFeatures	Clinical Features
clinicalManagement	Clinical Management
cloning	Cloning and Expression
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:

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			comma list of ClinVar accession
					dbSnps			comma delimited list of SNPs
					gnomadSnps			gnomAD SNPs
			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
					references
					comments
					mouseGeneSymbol
					mouseMgiID
					approvedGeneSymbols
					geneIDs
					ensemblIDs
					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
					approvedGeneSymbols
					geneIDs
					ensemblIDs
			externalLinks
				geneIDs				comma delimited list of entrez gene IDs
				hgncID				HGNC ID
				ensemblIDs				triple-colon delimited list of coma-delimited ensembl ID pairs
				approvedGeneSymbols				comma delimited list of approved gene symbols
				ncbiReferenceSequences				comma delimited list of NCBI reference sequences
				genbankNucleotideSequences				comma delimited list of genbank nucleotide sequences
				proteinSequences				comma delimited list of protein sequences
				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
				hprdIDs				comma delimited list of hprd IDs
				coriellDiseases				triple semi-colon delimited list of double semi-colon delimited coriell disease
				orphanetDiseases				triple semi-colon delimited list of double semi-colon delimited orphanet ID/disease pairs
				ordrDiseases				GARD/ORDR diseases
				decipherSyndromes				DECIPHER syndromes
				decipherGene				DECIPHER gene flag (true\|false)
				geneticsHomeReferenceIDs				Genetics Home Reference IDs
				omiaIDs				OMIA IDs
				snomedctIDs				SNOMEDCT IDs
				icd10cmIDs				ICD10CM IDs
				icd9cmIDs				ICD9CM IDs
				umlsIDs				UMLS IDs
				diseaseOntologyIDs				Disease Ontology IDs
				geneticAllianceIDs				Genetic Alliance IDs
				gtr				GTR
				cmgGene				CMG Gene
				keggPathways				KEGG Pathways
				gwasCatalog				GWAS Catalog
				clinGenDosage				ClinGen Dosage
				clinGenValidity				ClinGen Validity
				monarch				Monarch
				newbornScreening				Newborn Screening
				pharmgkbID				PharmgKB ID
			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
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:

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:

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
				references
				comments
				mouseGeneSymbol
				mouseMgiID
				approvedGeneSymbols
				geneIDs
				ensemblIDs
				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

'status' Handler

The 'status' handler can be used to check the API status.

For example:

https://api.omim.org/api/status

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.

NOTE: OMIM is intended for use primarily by physicians and other professionals concerned with genetic disorders, by genetics researchers, and by advanced students in science and medicine. While the OMIM database is open to the public, users seeking information about a personal medical or genetic condition are urged to consult with a qualified physician for diagnosis and for answers to personal questions.
OMIM^® and Online Mendelian Inheritance in Man^® are registered trademarks of the Johns Hopkins University.
Copyright^® 1966-2023 Johns Hopkins University.
Printed: June 2, 2023