PhenoImageShare API Documentation

Base URL www.phenoimageshare.org/data/rest/


/getImages

This method should be the main one used to explore the data. If you find a parameter missing, please contact us on webmaster@phenoimageshare.org .

Examples

1. Get "eye" images, restrict the result number to 5.

$ curl 'http://www.phenoimageshare.org/data/rest/getImages?term=eye&resultNo=5' -i -H 'Accept: application/json'

2. Get images with eye phenotypes in post natal females.

$ curl ' http://www.phenoimageshare.org/data/rest/getImages?phenotype=eye&sex=FEMALE&stage=postnatal%20stage&resultNo=1' -i -H 'Accept: application/json'

3. Get mouse images associated with genetic features located on chromosome 2.

$ curl ' http://www.phenoimageshare.org/data/rest/getImages?chromosome=2&taxon=Mus%20musculus&resultNo=10' -i -H 'Accept: application/json'

4. Get "eye" images, that are not annotated neither with heart, nor with liver.

$ curl 'http://www.phenoimageshare.org/data/rest/getImages?term=eye&-anatomy=liver&-anatomy=heart' -i -H 'Accept: application/json'

5. Get images of "lens vesicle" or "heart", but pioritize images of lens vesicle first.

$ curl 'http://www.phenoimageshare.org/data/rest//getImages?anatomy=lens%20vesicle^1&anatomy=heart^2&resNo=70' -i -H 'Accept: application/json'

Parameters
Name Type Required Description Default Example Values
term String false Term to search in any searchable field. Can be id or text for any field accessible. These are anatomy, gene and phenotype fields as well as image source and image visualization method, sample preparation. * eye
phenotype String false Images depicting the phenotype term passed. * MP:0010254
anatomy String[] false Images depicting the given anatomical structure, regardless of abnormalities. You can request to prioritize certain queries with ^[desired_position], see example above. Default position is 0. These values are used to boost the queries so the order cannot be guaranteed. * MA:0000261, eye
-anatomy String[] false Images NOT depicting the given anatomical structure, with or without of abnormalities. * MA:0000261, eye
gene String false Use mutantGene instead. Filters for samples with a mutation in the specified gene. * MGI:1891295, Spns2
mutantGene String false Filters for samples with a mutation in the specified gene. * MGI:1891295, Spns2
expressedFeature String false Filters for images depicting expression of the specified feature (gene or allele symbol or id). * Sesn3
sex String false Returns only images of samples with the specified sex. * FEMALE , MALE
taxon String false NCBI id or text / label of a taxon. * Mus musculus
sampleType String false For mutant/wildType facet filtering. * WILD_TYPE or MUTANT
imageType String false Filter on expression or anatomy/phenotype images for faceting. * EXPRESSION , PHENOTYPE_ANATOMY
stage String false Stage ontology id or text. * postnatal stage , MmusDv_0000092
samplePreparation String false Label or id of a child of Sample Preparation in FBBI ontology. * living tissue
imagingMethod String false Label or id of a child of Imaging Method in FBBI ontology. * macroscopy
visualisationMethod String false Label or id of a child of Visualisation Method in FBBI ontology. * fluorescent protein tag
position Long false Position for genomic search. For better results with point mutations use interval search defined by startPosition and endPosition. * 91008288
startPosition Long false Start position for genomic location interval search. * 91008288
endPosition Long false End position for genomic location interval search. * 91018288
chromosome String false Chromosome for genomic location search. * X
strand String false Strand for genomic location search. * -
resultNo Integer false Number of result objects to be returned back. 100
hostName String false Name of the website/resource hosting the images. * Mouse Atlas EMAGE
start Integer false Start position to return the results. Useful for pagination. 0
lastRoiEditAfter Date false Get images with ROIs/annotations edited after the given date. (none) 1976-03-06T23:59:59.999Z
lastRoiEditBefore Date false Get images with ROIs/annotations edited before the given date.Please note that not all annotations are provided to us with a date, so this method might return incomplete annotation sets. (none) 2016-03-06T23:59:59.999Z

/getImage

Examples

Get image with id 6_image_VFB_00009318.

$ curl ' http://www.phenoimageshare.org/data/rest/getImage?imageId=6_image_VFB_00009318 ' -i -H 'Accept: application/json'

Parameters
Name Type Required Description Default Example Values
imageId String true Image document with the specified id. (none) 6_image_VFB_00009318

/getImageDetails

Parameters
Name Type Required Description Default Example Values
imageId String true Image document with the specified id. (none) 6_image_VFB_00009318

/getRois

Examples

1. Get all annotations for image 6_image_VFB_00009318. Note that there is a default limit of results, so in order to get all documents back, just provide a high result limit.

$ curl 'http://www.phenoimageshare.org/data/rest/getRois?imageId=6_image_VFB_00009318&resultNo=10000000' -i -H 'Accept: application/json'

2. Get annotations created after January 2012. The date must be provided in Zulu time. Please note that most annotations provided to us by our collaborators usually don't have the annotation date, so this will only query a small subset of annotations with the date provided.

$ curl 'http://www.phenoimageshare.org/data/rest/getRois?createdAfter=2010-01-01T00:00:00.000Z' -i -H 'Accept: application/json'

Parameters
Name Type Required Description Default Example Values
imageId String false ROI associated to the image. * 6_image_VFB_00009318
userId String false Id of the user who created the annotation. (none) user_021897401
userGroupId String false Group to which the user belongs. (none) groupA
lastEditBefore Date false Get annotations edited before the given date. (none) 2016-03-06T23:59:59.999Z
lastEditAfter Date false Get annotations edited after the given date. (none) 1976-03-06T23:59:59.999Z
createdBefore Date false Get annotations created before the given date. Please note that not all annotations are provided to us with a date, so this method might return incomplete annotation sets. (none) 2016-03-06T23:59:59.999Z
createdAfter Date false Get annotations created after the given date. Please note that not all annotations are provided to us with a date, so this method might return incomplete annotation sets. (none) 1976-03-06T23:59:59.999Z
resultNo Integer false Number of result objects to be returned back. 100
start Integer false Start position to return the results. Useful for pagination. 0

/getRoi

Examples

Get roi with id 4_roi_VFB_00022854-b.

$ curl ' http://www.phenoimageshare.org/data/rest/getRoi?roiId=4_roi_VFB_00022854-b' -i -H 'Accept: application/json'

Parameters
Name Type Required Description Default Example Values
roiId String true ROI with the specified id. (none) 4_roi_roi_VFB_00022854-b

/getChannel

Examples

Get channel with id 4_channel_VFB_00022854-b.

$ curl 'http://www.phenoimageshare.org/data/rest/getChannel?channelId=4_channel_VFB_00022854-b' -i -H 'Accept: application/json'

Parameters
Name Type Required Description Default Example Values
channelId String true Channel with the specified id. (none) 4_channel_VFB_00022854-b

/getChannels

Channels contain information about the visualization method, i.e. type of fluorescent marker used or the gene whose expression is to be seen in the rois associated to this channel.

Examples

Get chanels for image with id 4_image_VFB_00022854.

$ curl ' http://www.phenoimageshare.org/data/rest/getChannels?imageId=4_image_VFB_00022854 ' -i -H 'Accept: application/json'

Parameters
Name Type Required Description Default Example Values
imageId String true Channel with the specified id. * 4_image_VFB_00022854
resultNo Integer false Number of result objects to be returned back. 100
start Integer false Start position to return the results. Useful for pagination. 0

/getAutosuggest

Returns a JSONArray of suggestions for the typed string.

Examples

1. Get 20 generic autosuggest options for the string "ab".

$ curl ' http://www.phenoimageshare.org/data/rest/getAutosuggest?term=ab&resultNo=20' -i -H 'Accept: application/json'

Result example:

{ "response": { "suggestions":["Abt1","Abcd1","Abcb6","Abhd5","Abca4","Abtb2","Ablim1","Abhd17a","absent tail","abdominal aorta","abnormal hair cycle","abnormal head shape","abnormal incisor color","abdominal segment skin","abnormal ear rotation","Abcd1","abnormal coat appearance","abnormal lens morphology","abnormal nail morphology","abnormal iris pigmentation"] } }

2. Get gene suggestion options for the string "ab".

$ curl 'http://www.phenoimageshare.org/data/rest/getAutosuggest?term=ab&autosuggestType=GENE' -i -H 'Accept: application/json'

Parameters
Name Type Required Description Default Example Values
term String false JSON array of suggested terms. To be used with the "type" parameter for specific autosuggests. * abn
autosuggestType String false Possible values are [GENE, ANATOMY, PHENOTYPE]. If one is specified autosuggest will be typed (i.e. return only gene names matching th typed string). If left out autosuggest will be in generic mode. * GENE
stage String false Restricts results for autosuggest to documents for the stage passed. * postnatal stage
imagingMethod String false Restricts results for autosuggest to documents for the imaging method passed. * X-ray illumination
taxon String false Restricts results for autosuggest to documents for the taxon passed. * Mus musculus
sampleType String false Restricts results for autosuggest to documents for the sampleType passed. * MUTANT
imageGeneratedBy String false Restricts results for autosuggest to documents for images generated by the passed institute. * WTSI
hostName String false Restricts results for autosuggest to documents hosted on the website provided. * IMPC Portal
resultNo Integer false Max number of suggestions to be returned. It is not recommended to put a bigger number than you actually need as the time cost increses quite significanlty with it. 10 20

/getComplexAutosuggest

Returns a JSONArray of suggestions for autosuggest. Like /getAutosuggest but offers more info on the term such as ontology id, type of annotation in which it is used and synonyms when available.

Get 5 autosuggest options for the string "ab".

$ curl 'http://www.phenoimageshare.org/data/rest/getComplexAutosuggest?term=ab&resultNo=5' -i -H 'Accept: application/json'

Result example:

{ response: { suggestions: [ { autosuggest_term_id: "MGI:1353636", autosuggest_type: "GENE", autosuggest_term_label: "Abt1" }, { autosuggest_term_id: "MGI:1349215", autosuggest_type: "GENE", autosuggest_term_label: "Abcd1" }, { autosuggest_term_id: "MGI:1921354", autosuggest_type: "GENE", autosuggest_term_label: "Abcb6" }, { autosuggest_term_id: "MGI:1914719", autosuggest_type: "GENE", autosuggest_term_label: "Abhd5" }, { autosuggest_term_id: "MGI:109424", autosuggest_type: "GENE", autosuggest_term_label: "Abca4" } ] } }

Get gene autosuggest options for the string "ab".

$ curl 'http://www.phenoimageshare.org/data/rest/getComplexAutosuggest?term=ab&type=GENE' -i -H 'Accept: application/json'

Parameters
Name Type Required Description Default Example Values
term String false JSON array of suggested terms. To be used with the "type" parameter for specific autosuggests. * abn
autosuggestType String false Possible values are [GENE, ANATOMY, PHENOTYPE]. If one is specified autosuggest will be typed (i.e. return only gene names matching th typed string). If left out autosuggest will be in generic mode. * GENE
stage String false Restricts results for autosuggest to documents for the stage passed. * postnatal stage
imagingMethod String false Restricts results for autosuggest to documents for the imaging method passed. * X-ray illumination
taxon String false Restricts results for autosuggest to documents for the taxon passed. * Mus musculus
sampleType String false Restricts results for autosuggest to documents for the sampleType passed. * MUTANT
imageGeneratedBy String false Restricts results for autosuggest to documents for images generated by the passed institute. * WTSI
resultNo Integer false Max number of suggestions to be returned. It is not recommended to put a bigger number than you actually need as the time cost increses quite significanlty with it. 10 20

/getDataReleases

Examples

Get information about all public (live) releases.

$ curl 'http://www.phenoimageshare.org/data/rest/getDataReleases' -i -H 'Accept: application/json'

Parameters
No parameters supported.

/similar

Examples

Get images similar to image with id 4_image_VFB_00022854.

$ curl 'http://www.phenoimageshare.org/data/rest/similar?imageId=4_image_VFB_00022854' -i -H 'Accept: application/json'

Parameters
Name Type Required Description Default Example Values
imageId String true Id of the image of interest. Phenotype and anatomy fields will be used in search for similar images. * 4_image_VFB_00022854
resultNo Integer false Max number of results to be returned. Can be used with "start" for pagination. 10 20
start Integer false Start position to return the results. Useful for pagination. 0

/download

Examples

Get tab separated details image with id 4_image_VFB_00022854.

$ curl 'http://www.phenoimageshare.org/data/rest/download?imageId=4_image_VFB_00022854' -i -H 'Accept: application/json'

Parameters
Name Type Required Description Default Example Values
imageId String false Id of the image to download details for. * 4_image_VFB_00022854
All parameters from getImages/ are applied in the same way.