Hooks -- owlSimFunction and geneList

yuanzhou commented 8 years ago

See https://github.com/monarch-initiative/monarch-app/issues/970

kshefchek commented 8 years ago

@yuanzhou I'm curious if you have a time line for getting this fix in. A few features on our analyze phenotypes page are dependent on this, specifically the "compare to gene list" option and upload/paste functionality. We have the option of simply disabling these settings if we are far away from a fix.

harryhoch commented 8 years ago

@yuanzhou, would this be hard to do? Sounds like it would be worth a bit of effort to help things out... How much work is required?

yuanzhou commented 8 years ago

@kshefchek I didn't realize that "Upload" has something to do with Exomiser since I never really played with that. I'll look into this by playing with the two example input files and get this fixed in Phenogrid.

Is this also related to geneList? Or only used by Exomiser?

@harryhoch right now I have no idea of the details, I think it's a good time to get this hook fixed in phenogrid. Glad you showed me some basic things about Exomiser couple weeks ago.

harryhoch commented 8 years ago

ok. @kshefchek, please help @yuanzhou with details. Pull me in as needed.

yuanzhou commented 8 years ago

@kshefchek can you also address the installation/running monarch server issue first? https://github.com/monarch-initiative/monarch-app/issues/1047

I just tried another fresh installation again and saw the same error message. I'm sure I'll need to have monarch running to play with the Exomiser related functionalities. Thanks!

kshefchek commented 8 years ago

Here are the two use cases we want to support:

Pass a list of genes to phenogrid, in this case, use the compare call rather than simsearch to generate the phenogrid view, see: https://github.com/monarch-initiative/phenogrid/blob/c008e5/js/phenogrid.js#L1058

This should be similar to calls to compare for the genotype expansion.

Pass a phenogrid compatible json object directly into phenogrid. This was initially used to pass exomiser output into phenogrid, but ideally any JSON structure compatible with the phenogrid data model should be accepted and displayed. The idea here is that a widget that manages uploading/pasting of raw similarity data could then be passed into phenogrid and displayed. I can point to what this looked like pre-refactor, but I'm assuming we can pass the json directly to the data manager class and skip the data loader class?

yuanzhou commented 8 years ago

This is really helpful @kshefchek. I can handle the geneList case very easily since I got the genotype expansion work with the compare API. And I'm assuming this is the currently disabled compare section:

capture

For the exomiser related upload section, couple of questions:

Does the uploaded file have the same JSON structure as the example 1 or 2, or it doesn't matter as long as it's a valid raw similarity data? My understanding is at least there needs to be a pre-defined JOSN filed as the target input of phenogrid. But I didn't see Example 1 and 2 share any common field.
Phenogrid only takes a list of phenotype IDs as input. Does this mean we'll only need to parse the JSON file and use the phenotype_list from Example 1 (it's another compatible JSON format) or a.id_list from Example 2 (seems like a simsearch result JSON) for generating a phenogrid view?

capture

Phenogrid only parses the simsearch format like Example 2, if it's Example 1, phenogrid will need to use the phenotype list to load the corresponding simsearch JSON.

kshefchek commented 8 years ago

    And I'm assuming this is the currently disabled compare section:

that's correct

    Phenogrid only parses the simsearch format like Example 2, if it's Example 1, phenogrid will need to use the phenotype list to load the corresponding simsearch JSON.

I think that is fine. Both examples used to work but we can make a new one for example 1. Do we have documentation on what JSON schema (not sure if right terminology) is needed for phenogrid to work?

yuanzhou commented 8 years ago

@kshefchek Here is the simsearch JSON schema required by Phenogrid: https://github.com/monarch-initiative/phenogrid/blob/master/tests/mocha/simsearch-schema.json But this schema is inconsistent with Example 1 and 2.

Here is a real simsearch output for Phenogrid:

{"b":[{"id":"ZFIN:ZDB-GENE-040426-1664","label":"pde6c","type":"gene","matches":[{"b":{"id":"ZP:0006003","IC":14.693865774103203,"label":"abnormal(ly) degenerate retinal cone cell"},"a":{"id":"HP:0000510","IC":7.478994437324813,"label":"Rod-cone dystrophy"},"lcs":{"id":"MP:0001326","IC":6.1210198870199966,"label":"retinal degeneration"}},{"b":{"id":"ZP:0005796","IC":13.037903273382044,"label":"abnormal(ly) arrested visual perception"},"a":{"id":"HP:0000618","IC":6.942385674597757,"label":"Blindness"},"lcs":{"id":"ZP:0001865","IC":5.450940772660889,"label":"abnormal(ly) decreased process quality visual perception"}}],"score":{"metric":"combinedScore","score":37,"rank":0},"taxon":{"id":"NCBITaxon:7955","label":"Danio rerio"}},{"id":"ZFIN:ZDB-GENE-011128-7","label":"gucy2f","type":"gene","matches":[{"b":{"id":"ZP:0001866","IC":13.635865774103202,"label":"abnormal(ly) dystrophic retina"},"a":{"id":"HP:0000510","IC":7.478994437324813,"label":"Rod-cone dystrophy"},"lcs":{"id":"HP:0000556","IC":6.710975178494684,"label":"Retinal dystrophy"}},{"b":{"id":"MP:0006149","IC":5.450940772660889,"label":"decreased visual acuity"},"a":{"id":"HP:0000618","IC":6.942385674597757,"label":"Blindness"},"lcs":{"id":"ZP:0001865","IC":5.450940772660889,"label":"abnormal(ly) decreased process quality visual perception"}}],"score":{"metric":"combinedScore","score":34,"rank":1},"taxon":{"id":"NCBITaxon:7955","label":"Danio rerio"}},{"id":"ZFIN:ZDB-GENE-040718-194","label":"olfm1a","type":"gene","matches":[{"b":{"id":"ZP:0006699","IC":14.661865774103203,"label":"abnormal(ly) decreased length cranial nerve II axon"},"a":{"id":"HP:0000648","IC":6.199237546466478,"label":"Optic atrophy"},"lcs":{"id":"HP:0000587","IC":5.308526743963795,"label":"Abnormality of the optic nerve"}},{"b":{"id":"ZP:0006697","IC":14.647865774103202,"label":"abnormal(ly) degenerate retinal inner nuclear layer cell"},"a":{"id":"HP:0000510","IC":7.478994437324813,"label":"Rod-cone dystrophy"},"lcs":{"id":"MP:0001326","IC":6.1210198870199966,"label":"retinal degeneration"}},{"b":{"id":"ZP:0006694","IC":12.30293767921584,"label":"abnormal(ly) delayed eye development"},"a":{"id":"HP:0001249","IC":4.383453581314417,"label":"Intellectual disability"},"lcs":{"id":"HP:0012759","IC":3.1306986403788106,"label":"Neurodevelopmental abnormality"}},{"b":{"id":"ZP:0001232","IC":10.8065108520456,"label":"abnormal(ly) degenerate brain"},"a":{"id":"HP:0002074","IC":11.28493767921584,"label":"Increased neuronal autofluorescent lipopigment"},"lcs":{"id":"HP:0007367","IC":4.250616392157961,"label":"Atrophy/Degeneration affecting the central nervous system"}}],"score":{"metric":"combinedScore","score":33,"rank":2},"taxon":{"id":"NCBITaxon:7955","label":"Danio rerio"}},{"id":"ZFIN:ZDB-GENE-070112-2132","label":"napbb","type":"gene","matches":[{"b":{"id":"ZP:0001868","IC":11.633865774103203,"label":"abnormal(ly) arrested optokinetic behavior"},"a":{"id":"HP:0000550","IC":10.152434155465906,"label":"Undetectable electroretinogram"},"lcs":{"id":"MP:0005253","IC":3.2729172089009055,"label":"abnormal eye physiology"}},{"b":{"id":"ZP:0005995","IC":13.675865774103203,"label":"abnormal(ly) degenerate retina photoreceptor cell"},"a":{"id":"HP:0000510","IC":7.478994437324813,"label":"Rod-cone dystrophy"},"lcs":{"id":"MP:0001326","IC":6.1210198870199966,"label":"retinal degeneration"}}],"score":{"metric":"combinedScore","score":33,"rank":3},"taxon":{"id":"NCBITaxon:7955","label":"Danio rerio"}},{"id":"ZFIN:ZDB-GENE-030318-2","label":"chm","type":"gene","matches":[{"b":{"id":"ZP:0001773","IC":12.051903273382045,"label":"abnormal(ly) degenerate retina"},"a":{"id":"HP:0000510","IC":7.478994437324813,"label":"Rod-cone dystrophy"},"lcs":{"id":"MP:0001326","IC":6.1210198870199966,"label":"retinal degeneration"}},{"b":{"id":"ZP:0003211","IC":10.714975178494685,"label":"abnormal(ly) delayed hatching"},"a":{"id":"HP:0001249","IC":4.383453581314417,"label":"Intellectual disability"},"lcs":{"id":"HP:0012759","IC":3.1306986403788106,"label":"Neurodevelopmental abnormality"}},{"b":{"id":"ZP:0004750","IC":12.297937679215838,"label":"abnormal(ly) disrupted visual perception"},"a":{"id":"HP:0000618","IC":6.942385674597757,"label":"Blindness"},"lcs":{"id":"ZP:0010561","IC":5.4339904311949185,"label":"abnormal(ly) process quality visual perception"}},{"b":{"id":"HP:0010831","IC":3.8751914501010685,"label":"Impaired proprioception"},"a":{"id":"HP:0001251","IC":4.866702885548184,"label":"Ataxia"},"lcs":{"id":"ZP:0000207","IC":3.8751914501010685,"label":"abnormal(ly) quality neuromuscular process controlling balance"}}],"score":{"metric":"combinedScore","score":32,"rank":4},"taxon":{"id":"NCBITaxon:7955","label":"Danio rerio"}},{"id":"ZFIN:ZDB-GENE-050119-2","label":"lrp2a","type":"gene","matches":[{"b":{"id":"ZP:0007448","IC":14.642865774103203,"label":"abnormal(ly) increased diameter optic nerve head"},"a":{"id":"HP:0000648","IC":6.199237546466478,"label":"Optic atrophy"},"lcs":{"id":"HP:0000587","IC":5.308526743963795,"label":"Abnormality of the optic nerve"}},{"b":{"id":"ZP:0007439","IC":14.638865774103202,"label":"abnormal(ly) hypotrophic retinal inner nuclear layer"},"a":{"id":"HP:0000510","IC":7.478994437324813,"label":"Rod-cone dystrophy"},"lcs":{"id":"MP:0003727","IC":4.669124526916715,"label":"abnormal retinal layer morphology"}},{"b":{"id":"MP:0006149","IC":5.450940772660889,"label":"decreased visual acuity"},"a":{"id":"HP:0000618","IC":6.942385674597757,"label":"Blindness"},"lcs":{"id":"ZP:0001865","IC":5.450940772660889,"label":"abnormal(ly) decreased process quality visual perception"}}],"score":{"metric":"combinedScore","score":30,"rank":5},"taxon":{"id":"NCBITaxon:7955","label":"Danio rerio"}},{"id":"ZFIN:ZDB-GENE-020419-38","label":"terfa","type":"gene","matches":[{"b":{"id":"ZP:0001773","IC":12.051903273382045,"label":"abnormal(ly) 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rerio"}},{"id":"ZFIN:ZDB-GENE-060312-41","label":"ush1c","type":"gene","matches":[{"b":{"id":"ZP:0008132","IC":14.664865774103202,"label":"abnormal(ly) bent auditory receptor cell kinocilium"},"a":{"id":"HP:0000648","IC":6.199237546466478,"label":"Optic atrophy"},"lcs":{"id":"MP:0002752","IC":3.669912881908487,"label":"abnormal somatic nervous system morphology"}},{"b":{"id":"ZP:0008133","IC":14.665865774103203,"label":"abnormal(ly) detached from retinal cone cell presynaptic cytoskeletal matrix assembled at active zones towards retinal outer plexiform layer postsynaptic density"},"a":{"id":"HP:0000510","IC":7.478994437324813,"label":"Rod-cone dystrophy"},"lcs":{"id":"UBERON:0001781PHENOTYPE","IC":4.52608749611779,"label":"layer of retina phenotype"}},{"b":{"id":"ZP:0008129","IC":13.634865774103202,"label":"abnormal(ly) disrupted detection of light stimulus involved in visual perception"},"a":{"id":"HP:0000618","IC":6.942385674597757,"label":"Blindness"},"lcs":{"id":"GO:0007601PHENOTYPE","IC":4.566066811525935,"label":"visual perception phenotype"}},{"b":{"id":"ZP:0000200","IC":11.021903273382046,"label":"abnormal(ly) disrupted startle response"},"a":{"id":"HP:0001251","IC":4.866702885548184,"label":"Ataxia"},"lcs":{"id":"GO:0050905PHENOTYPE","IC":3.821610458911279,"label":"neuromuscular process phenotype"}}],"score":{"metric":"combinedScore","score":25,"rank":92},"taxon":{"id":"NCBITaxon:7955","label":"Danio rerio"}},{"id":"ZFIN:ZDB-GENE-030131-443","label":"atp6v0b","type":"gene","matches":[{"b":{"id":"ZP:0001773","IC":12.051903273382045,"label":"abnormal(ly) degenerate retina"},"a":{"id":"HP:0000510","IC":7.478994437324813,"label":"Rod-cone dystrophy"},"lcs":{"id":"MP:0001326","IC":6.1210198870199966,"label":"retinal degeneration"}}],"score":{"metric":"combinedScore","score":25,"rank":93},"taxon":{"id":"NCBITaxon:7955","label":"Danio rerio"}},{"id":"ZFIN:ZDB-GENE-991117-1","label":"glra1","type":"gene","matches":[{"b":{"id":"ZP:0006794","IC":13.623865774103203,"label":"abnormal(ly) sporadic tonic skeletal muscle contraction"},"a":{"id":"HP:0001336","IC":7.4923144217044095,"label":"Myoclonus"},"lcs":{"id":"HP:0004305","IC":6.148190559711159,"label":"Involuntary movements"}},{"b":{"id":"ZP:0006792","IC":13.606865774103202,"label":"abnormal(ly) sporadic startle response"},"a":{"id":"HP:0001251","IC":4.866702885548184,"label":"Ataxia"},"lcs":{"id":"GO:0050905PHENOTYPE","IC":3.821610458911279,"label":"neuromuscular process phenotype"}}],"score":{"metric":"combinedScore","score":25,"rank":94},"taxon":{"id":"NCBITaxon:7955","label":"Danio rerio"}},{"id":"ZFIN:ZDB-GENE-080104-1","label":"lepr","type":"gene","matches":[{"b":{"id":"ZP:0001323","IC":9.125012677773526,"label":"abnormal(ly) disrupted brain development"},"a":{"id":"HP:0002059","IC":6.383938260659617,"label":"Cerebral atrophy"},"lcs":{"id":"MP:0000913","IC":3.0459096986877356,"label":"abnormal brain development"}},{"b":{"id":"ZP:0005361","IC":10.32593767921584,"label":"abnormal(ly) decreased thickness cranial nerve II"},"a":{"id":"HP:0000648","IC":6.199237546466478,"label":"Optic atrophy"},"lcs":{"id":"MP:0001330","IC":5.484660849160973,"label":"abnormal optic nerve morphology"}},{"b":{"id":"ZP:0003139","IC":11.178434155465906,"label":"abnormal(ly) decreased size retinal ganglion cell layer"},"a":{"id":"HP:0000510","IC":7.478994437324813,"label":"Rod-cone dystrophy"},"lcs":{"id":"MP:0003727","IC":4.669124526916715,"label":"abnormal retinal layer morphology"}}],"score":{"metric":"combinedScore","score":25,"rank":95},"taxon":{"id":"NCBITaxon:7955","label":"Danio rerio"}},{"id":"ZFIN:ZDB-GENE-060825-69","label":"llgl1","type":"gene","matches":[{"b":{"id":"ZP:0000359","IC":9.368938260659617,"label":"abnormal(ly) decreased size forebrain"},"a":{"id":"HP:0002059","IC":6.383938260659617,"label":"Cerebral atrophy"},"lcs":{"id":"MP:0000774","IC":4.996840976795849,"label":"decreased brain size"}},{"b":{"id":"ZP:0008388","IC":11.466940772660891,"label":"abnormal(ly) structure retinal neural layer"},"a":{"id":"HP:0000510","IC":7.478994437324813,"label":"Rod-cone dystrophy"},"lcs":{"id":"MP:0003727","IC":4.669124526916715,"label":"abnormal retinal layer morphology"}},{"b":{"id":"ZP:0001397","IC":11.151434155465907,"label":"abnormal(ly) delayed retina layer formation"},"a":{"id":"HP:0001249","IC":4.383453581314417,"label":"Intellectual disability"},"lcs":{"id":"HP:0012759","IC":3.1306986403788106,"label":"Neurodevelopmental abnormality"}},{"b":{"id":"ZP:0001276","IC":11.308937679215841,"label":"abnormal(ly) disorganized retina cell"},"a":{"id":"HP:0000608","IC":9.44994077266089,"label":"Macular degeneration"},"lcs":{"id":"HP:0000479","IC":3.8095108520455985,"label":"Abnormality of the retina"}}],"score":{"metric":"combinedScore","score":25,"rank":96},"taxon":{"id":"NCBITaxon:7955","label":"Danio rerio"}},{"id":"ZFIN:ZDB-GENE-980526-400","label":"otx1b","type":"gene","matches":[{"b":{"id":"ZP:0000359","IC":9.368938260659617,"label":"abnormal(ly) decreased size forebrain"},"a":{"id":"HP:0002059","IC":6.383938260659617,"label":"Cerebral atrophy"},"lcs":{"id":"MP:0000774","IC":4.996840976795849,"label":"decreased brain size"}},{"b":{"id":"ZP:0009725","IC":13.046903273382044,"label":"abnormal(ly) separated from retinal pigmented epithelium anterior side towards retinal pigmented epithelium posterior side"},"a":{"id":"HP:0000510","IC":7.478994437324813,"label":"Rod-cone dystrophy"},"lcs":{"id":"UBERON:0001782PHENOTYPE","IC":5.462874662022973,"label":"pigmented layer of retina phenotype"}}],"score":{"metric":"combinedScore","score":25,"rank":97},"taxon":{"id":"NCBITaxon:7955","label":"Danio rerio"}},{"id":"ZFIN:ZDB-GENE-991026-3","label":"tyr","type":"gene","matches":[{"b":{"id":"ZP:0000597","IC":11.47794077266089,"label":"abnormal(ly) decreased pigmentation retinal pigmented epithelium"},"a":{"id":"HP:0000510","IC":7.478994437324813,"label":"Rod-cone dystrophy"},"lcs":{"id":"MP:0005201","IC":5.572169842415648,"label":"abnormal retinal pigment epithelium morphology"}}],"score":{"metric":"combinedScore","score":25,"rank":98},"taxon":{"id":"NCBITaxon:7955","label":"Danio rerio"}},{"id":"ZFIN:ZDB-GENE-040718-106","label":"rbpms2a","type":"gene","matches":[{"b":{"id":"ZP:0006432","IC":13.629865774103203,"label":"abnormal(ly) increased process quality optomotor response"},"a":{"id":"HP:0000550","IC":10.152434155465906,"label":"Undetectable electroretinogram"},"lcs":{"id":"MP:0005253","IC":3.2729172089009055,"label":"abnormal eye physiology"}},{"b":{"id":"ZP:0006434","IC":13.652865774103203,"label":"abnormal(ly) decreased branchiness amacrine cell dendrite"},"a":{"id":"HP:0000510","IC":7.478994437324813,"label":"Rod-cone dystrophy"},"lcs":{"id":"UBERON:0001781PHENOTYPE","IC":4.52608749611779,"label":"layer of retina phenotype"}}],"score":{"metric":"combinedScore","score":25,"rank":99},"taxon":{"id":"NCBITaxon:7955","label":"Danio rerio"}}],"metadata":{"maxSumIC":"11230.55214","meanMaxIC":"10.61382","meanMeanIC":"7.67619","meanSumIC":"135.34235","maxMaxIC":"14.74287","meanN":"17.62988","individuals":"24711","metric_stats":{"metric":"combinedScore","maxscore":"100","avgscore":"60","stdevscore":"4.32","comment":"These stats are approximations for this release"}},"resource":"OWLSim Server: http://owlsim.crbs.ucsd.edu/","a":["HP:0000510","HP:0000529","HP:0000550","HP:0000608","HP:0000618","HP:0000648","HP:0000709","HP:0000716","HP:0000726","HP:0000739","HP:0001249","HP:0001250","HP:0001251","HP:0001260","HP:0001300","HP:0001317","HP:0001336","HP:0001922","HP:0002059","HP:0002071","HP:0002074","HP:0002352","HP:0002361","HP:0002367","HP:0002505","HP:0003205","HP:0003208","HP:0003226","HP:0003463","HP:0003657","HP:0008765"],"cutoff":100,"apiVersionInfo":"monarch-api-2014-12-19"}

You may need to copy and paste it to a JSON viewer. a contains all the phenotype IDs in an array. That's what phenogrid needs from the upload file. Actually only a list of phenotype IDs is all we need from the upload, Phenogrid can always load the simsearch data using those phenotype IDs.

yuanzhou commented 8 years ago

IGNORE THIS

@kshefchek would it be too much work to have a compare api in POST? The initial data loading methods in phenogrid's dataLoader are tightly coupled. To make geneList work, I'll still need to reuse the dataLoader constructor and the related ajax POST as well as callbacks. The current compare API only does GET request with the phenotype id list and gene id list. Can you also add a POST version of this same comapre api? Then I can reuse the current dataLoader with adding less hooks. Thanks!

Another reason to use POST in addition to (or instead of) GET may be the URL length limitation that GET has.

yuanzhou commented 8 years ago

@kshefchek Ignore my request to have a POST compare api. I think I can reuse some of dataLoader methods by making corresponding changes for geneList.

One question: does this phenotypes and genes compare care about which species?

kshefchek commented 8 years ago

Since we're narrowing the search space by comparing to specific genes, this wouldn't require specifying species since gene ids are species specific.

yuanzhou commented 8 years ago

@kshefchek Thanks Kent. Sorry to say this, but after digging into the dataLoader code, I still think ajax POST version of the compare API makes more sense.

Can you please wrap the compare in a POST version like this:

For example:

URL: http://beta.monarchinitiative.org/compare/
POST data: phenotypes=HP:0000726+HP:0000746+HP:0001300&genes=NCBIGene:388552+NCBIGene:12166

The reason is phenogrid dataLoader's ajax GET method takes very different parameters and ajax POST is designed very specific to the way that how dataLoader should be used.

We should still keep the old compare GET api, since genotype expansion uses that format.

kshefchek commented 8 years ago

Sure, I've held off so far as the GET method has distinctions between grouping things with a plug sign versus a comma, maybe for the POST we can simplify it.

yuanzhou commented 8 years ago

@kshefchek

Since we're narrowing the search space by comparing to specific genes, this wouldn't require specifying species since gene ids are species specific.

Is it possible that we could use a fish gene and a mouse gene for this comparison? Or all the provided genes in geneList has to be for the same species? I asked this because when we transfer the raw simsearch data into Phenogrid dataLoder, species name is used to identify the target group. And this also affects several other UI displays, including the popup control panel. Because in the current phenogrid, we can check and uncheck species to add/hide their data.

I almost feel we need to customize many UI elements in Phenogrid to work with this geneList and upload.

kshefchek commented 8 years ago

The output from the compare call should theoretically include species name, are you finding some cases where this information is missing?

nlwashington commented 8 years ago

@yuanzhou you say that the "species name" is used to identify the target group. i would much prefer that the target group is specified by the config or user. the grouping could be done in any kind of way. here, the user has specified their groupings. in the case of user-specified gene list, i want to preserve my groupings in the way that i have given them to you. perhaps i even want to name my groupings. the phenogrid mechanism for groupings should be generic.

nlwashington commented 8 years ago

in the case of our existing example of simsearch, we've just already supplied the groupings to be conveniently set to species. but it would certainly be possible to re-group using other predefined things, like pathways, or gene families, or GO function, etc.

yuanzhou commented 8 years ago

@nlwashington agreed. And I've noticed some unexpected behaviors if the provided gene list contains genes from multiple species, since currently phenogrid grabs the simsearch data for per species based on the config file. And then the raw data gets transformed into a named array for each species. I'll work around this.

kshefchek commented 8 years ago

As far as the phenogrid internals, this would be similar to setting the species to "all" and ideally the UI would be driven by the output from the simsearch or compare. I know at one point "all species" meant human, mouse, zebrafish, is that still the case? Maybe we can use this to drive the use case of having a variable number of species show up in phenogrid, as I think we're also close to adding additional species to our owlsim server as well.

yuanzhou commented 8 years ago

You are right @kshefchek , I asked Mike for the phenogrid data structure and config details (since he started the refactoring) and he pointed me to a similar workaround. I used "compare" as the grouping name forgeneList case. And after some code tweaking I finally got it work with the compare mode.

I'll do more testing before making the commit. I'll prob commit directly in the monarch-app master branch since I'll only need to enable the "compare" section in the mustache file. I'll need @harryhoch 's review of the phenogrid changes before pushing it to phenogrid master.

And I figured out a way to work with the current compare api in ajax GET, so I think it's fine not to add that POST api for compare. But I've also noticed that this compare api doesn't always return the desired JSON structure.

kshefchek commented 8 years ago

great! I think I am seeing similar issues, is it when the compare function cannot find any similarities between the gene list and phenotypes? What should the output look like in this case?

yuanzhou commented 8 years ago

@kshefchek yes, for example: http://beta.monarchinitiative.org/compare/MP:0000433/NCBIGene:388552,NCBIGene:12166

it was working and returned the desired JSON data in the morning. While it only returned

{"a":{"id":"MP:0000433","label":"microcephaly","type":"phenotype","taxon":{},"id_list":["MP:0000433"]}}

this afternoon.

The desired JSON format should look like the JSON from simsearch/phenotype, here is a sample output:

{"b":[{"id":"ZFIN:ZDB-GENE-040718-29","label":"cldn7a","type":"gene","matches":[{"b":{"id":"ZP:0000054","IC":5.59477658364543,"label":"abnormal(ly) decreased size head"},"a":{"id":"MP:0000433","IC":4.054094985695492,"label":"microcephaly"},"lcs":{"id":"MP:0000433","IC":4.054094985695492,"label":"microcephaly"}}],"score":{"metric":"combinedScore","score":100,"rank":0},"taxon":{"id":"NCBITaxon:7955","label":"Danio rerio"}},{"id":"ZFIN:ZDB-GENE-041114-152","label":"ctdnep1b","type":"gene","matches":[{"b":{"id":"ZP:0000054","IC":5.59477658364543,"label":"abnormal(ly) decreased size head"},"a":{"id":"MP:0000433","IC":4.054094985695492,"label":"microcephaly"},"lcs":{"id":"MP:0000433","IC":4.054094985695492,"label":"microcephaly"}}],"score":{"metric":"combinedScore","score":100,"rank":1},"taxon":{"id":"NCBITaxon:7955","label":"Danio rerio"}},{"id":"ZFIN:ZDB-GENE-080806-1","label":"ralgapa1","type":"gene","matches":[{"b":{"id":"ZP:0000054","IC":5.59477658364543,"label":"abnormal(ly) decreased size head"},"a":{"id":"MP:0000433","IC":4.054094985695492,"label":"microcephaly"},"lcs":{"id":"MP:0000433","IC":4.054094985695492,"label":"microcephaly"}}],"score":{"metric":"combinedScore","score":93,"rank":2},"taxon":{"id":"NCBITaxon:7955","label":"Danio rerio"}},{"id":"ZFIN:ZDB-GENE-080103-2","label":"prlra","type":"gene","matches":[{"b":{"id":"ZP:0000054","IC":5.59477658364543,"label":"abnormal(ly) decreased size head"},"a":{"id":"MP:0000433","IC":4.054094985695492,"label":"microcephaly"},"lcs":{"id":"MP:0000433","IC":4.054094985695492,"label":"microcephaly"}}],"score":{"metric":"combinedScore","score":83,"rank":3},"taxon":{"id":"NCBITaxon:7955","label":"Danio rerio"}},{"id":"ZFIN:ZDB-GENE-030722-4","label":"slit1b","type":"gene","matches":[{"b":{"id":"ZP:0000054","IC":5.59477658364543,"label":"abnormal(ly) decreased size head"},"a":{"id":"MP:0000433","IC":4.054094985695492,"label":"microcephaly"},"lcs":{"id":"MP:0000433","IC":4.054094985695492,"label":"microcephaly"}}],"score":{"metric":"combinedScore","score":83,"rank":4},"taxon":{"id":"NCBITaxon:7955","label":"Danio rerio"}},{"id":"ZFIN:ZDB-GENE-030131-5174","label":"gabarapa","type":"gene","matches":[{"b":{"id":"ZP:0000117","IC":10.413938260659618,"label":"abnormal(ly) hypoplastic head"},"a":{"id":"MP:0000433","IC":4.054094985695492,"label":"microcephaly"},"lcs":{"id":"MP:0000433","IC":4.054094985695492,"label":"microcephaly"}}],"score":{"metric":"combinedScore","score":78,"rank":5},"taxon":{"id":"NCBITaxon:7955","label":"Danio rerio"}},{"id":"ZFIN:ZDB-GENE-081110-1","label":"rem2","type":"gene","matches":[{"b":{"id":"ZP:0000054","IC":5.59477658364543,"label":"abnormal(ly) decreased size head"},"a":{"id":"MP:0000433","IC":4.054094985695492,"label":"microcephaly"},"lcs":{"id":"MP:0000433","IC":4.054094985695492,"label":"microcephaly"}}],"score":{"metric":"combinedScore","score":77,"rank":6},"taxon":{"id":"NCBITaxon:7955","label":"Danio rerio"}},{"id":"ZFIN:ZDB-GENE-120809-2","label":"rlim","type":"gene","matches":[{"b":{"id":"ZP:0001143","IC":10.544402932852861,"label":"abnormal(ly) increased size head"},"a":{"id":"MP:0000433","IC":4.054094985695492,"label":"microcephaly"},"lcs":{"id":"MP:0011496","IC":3.713361810691726,"label":"abnormal head size"}}],"score":{"metric":"combinedScore","score":76,"rank":7},"taxon":{"id":"NCBITaxon:7955","label":"Danio rerio"}},{"id":"ZFIN:ZDB-GENE-040625-176","label":"trnt1","type":"gene","matches":[{"b":{"id":"ZP:0000407","IC":9.756975178494685,"label":"abnormal(ly) decreased width head"},"a":{"id":"MP:0000433","IC":4.054094985695492,"label":"microcephaly"},"lcs":{"id":"MP:0000433","IC":4.054094985695492,"label":"microcephaly"}}],"score":{"metric":"combinedScore","score":75,"rank":8},"taxon":{"id":"NCBITaxon:7955","label":"Danio rerio"}},{"id":"ZFIN:ZDB-GENE-050522-381","label":"tusc3","type":"gene","matches":[{"b":{"id":"ZP:0000054","IC":5.59477658364543,"label":"abnormal(ly) decreased size head"},"a":{"id":"MP:0000433","IC":4.054094985695492,"label":"microcephaly"},"lcs":{"id":"MP:0000433","IC":4.054094985695492,"label":"microcephaly"}}],"score":{"metric":"combinedScore","score":75,"rank":9},"taxon":{"id":"NCBITaxon:7955","label":"Danio rerio"}},{"id":"ZFIN:ZDB-GENE-040426-2087","label":"rngtt","type":"gene","matches":[{"b":{"id":"ZP:0000407","IC":9.756975178494685,"label":"abnormal(ly) decreased width head"},"a":{"id":"MP:0000433","IC":4.054094985695492,"label":"microcephaly"},"lcs":{"id":"MP:0000433","IC":4.054094985695492,"label":"microcephaly"}}],"score":{"metric":"combinedScore","score":75,"rank":10},"taxon":{"id":"NCBITaxon:7955","label":"Danio rerio"}},{"id":"ZFIN:ZDB-GENE-040830-1","label":"polb","type":"gene","matches":[{"b":{"id":"ZP:0000407","IC":9.756975178494685,"label":"abnormal(ly) decreased width head"},"a":{"id":"MP:0000433","IC":4.054094985695492,"label":"microcephaly"},"lcs":{"id":"MP:0000433","IC":4.054094985695492,"label":"microcephaly"}}],"score":{"metric":"combinedScore","score":75,"rank":11},"taxon":{"id":"NCBITaxon:7955","label":"Danio rerio"}},{"id":"ZFIN:ZDB-GENE-030131-899","label":"acadvl","type":"gene","matches":[{"b":{"id":"ZP:0000054","IC":5.59477658364543,"label":"abnormal(ly) decreased size head"},"a":{"id":"MP:0000433","IC":4.054094985695492,"label":"microcephaly"},"lcs":{"id":"MP:0000433","IC":4.054094985695492,"label":"microcephaly"}}],"score":{"metric":"combinedScore","score":75,"rank":12},"taxon":{"id":"NCBITaxon:7955","label":"Danio rerio"}},{"id":"ZFIN:ZDB-GENE-070912-300","label":"oc90","type":"gene","matches":[{"b":{"id":"ZP:0000054","IC":5.59477658364543,"label":"abnormal(ly) decreased size head"},"a":{"id":"MP:0000433","IC":4.054094985695492,"label":"microcephaly"},"lcs":{"id":"MP:0000433","IC":4.054094985695492,"label":"microcephaly"}}],"score":{"metric":"combinedScore","score":75,"rank":13},"taxon":{"id":"NCBITaxon:7955","label":"Danio rerio"}},{"id":"ZFIN:ZDB-GENE-041006-1","label":"gtf3aa","type":"gene","matches":[{"b":{"id":"ZP:0000054","IC":5.59477658364543,"label":"abnormal(ly) decreased size 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kshefchek commented 8 years ago

Any chance you could narrow down what we're missing specifically? Do we want an empty property "b" which has an empty list as a value? For example:

    {"b":[],"a":{"id":"MP:0000433","label":"microcephaly","type":"phenotype","taxon":{},"id_list":["MP:0000433"]}}

yuanzhou commented 8 years ago

"b" should contain all the matches. here is a quick example:

capture

Phenogrid parses the "b" to generate the grid cells. And "metadata" is used for color scale.

kshefchek commented 8 years ago

I switched our solr index back to an earlier version, so the compare queries should be working again now.

yuanzhou commented 8 years ago

@kshefchek did more testing, and this one didn't work.

http://beta.monarchinitiative.org/compare/HP:0011372+HP:0012594+MP:0000433/NCBIGene:616699,NCBIGene:9322

it only returned

{"a":{"label":"HP:0011372+HP:0012594+MP:0000433","id_list":["HP:0011372","HP:0012594","MP:0000433"]}}

Does this mean the simsearch didn't find any matches with the provided phenotypes and genes? Do we have a standard JSON to indicate that there's no data found?

kshefchek commented 8 years ago

That's correct, neither of these genes have any associated phenotypes so this is the default json that is returned. Do we need to make an update to the output?

yuanzhou commented 8 years ago

@kshefchek I see. No need to update the output format. I'll just check if the b part is in the resulting JSON. I'll assume no data found if b is missing.

yuanzhou commented 8 years ago

@kshefchek I added orthologs and paralogs for testing, there are matches, but the metadata (to be used for creating color scale) is missing. So I got the phenogrid view rendered by the grid cell colors are incorrect.

URL: http://beta.monarchinitiative.org/compare/HP:0012594+MP:0000433/NCBIGene:100856649,NCBIGene:616699,NCBIGene:257634,NCBIGene:791744,ZFIN:ZDB-GENE-980526-116,MGI:99783,ZFIN:ZDB-GENE-980526-347,ZFIN:ZDB-GENE-980526-116,MGI:99783,ZFIN:ZDB-GENE-980526-347

JSON response:

{"b":[{"id":"NCBIGene:791744","label":"lhx2b","type":"gene","matches":[{"b":{"id":"ZP:0000351","IC":12.629865774103203,"label":"abnormal(ly) aplastic postoptic commissure"},"a":{"id":"MP:0000433","IC":4.054094985695492,"label":"microcephaly"},"lcs":{"id":"HP:0002977","IC":3.551618648190776,"label":"Aplasia/Hypoplasia involving the central nervous system"}}],"score":{"metric":"combinedScore","score":15,"rank":3},"taxon":{"id":"NCBITaxon:7955","label":"Danio rerio"},"id_list":["ZP:0008043","ZP:0008042","ZP:0007610","ZP:0007609","ZP:0007603","ZP:0007604","ZP:0007605","ZP:0007606","ZP:0007607","ZP:0007608","ZP:0007484","ZP:0008046","ZP:0008047","ZP:0008044","ZP:0008045","ZP:0008048","ZP:0008049","ZP:0008050","ZP:0008052","ZP:0008051","ZP:0003027","ZP:0000213","ZP:0000985","ZP:0000945","ZP:0000966","ZP:0000115","ZP:0000351","ZP:0000368","ZP:0000337","ZP:0001365","ZP:0000965","ZP:0005796","ZP:0001000","ZP:0004816","ZP:0001559","ZP:0001995","ZP:0001840","ZP:0000029","ZP:0006648","ZP:0005044","ZP:0005398"]},{"id":"MGI:99783","label":"Lhx1","type":"gene","matches":[{"b":{"id":"MP:0000433","IC":4.054094985695492,"label":"microcephaly"},"a":{"id":"MP:0000433","IC":4.054094985695492,"label":"microcephaly"},"lcs":{"id":"MP:0000433","IC":4.054094985695492,"label":"microcephaly"}},{"b":{"id":"MP:0002966","IC":8.453940772660891,"label":"decreased circulating alkaline phosphatase level"},"a":{"id":"HP:0012594","IC":12.617865774103203,"label":"Microalbuminuria"},"lcs":{"id":"HP:0004364","IC":3.2599030098515027,"label":"Abnormality of nitrogen compound homeostasis"}}],"score":{"metric":"combinedScore","score":17,"rank":5},"taxon":{"id":"NCBITaxon:10090","label":"Mus musculus"},"id_list":["MP:0006032","MP:0011486","MP:0000913","MP:0006415","MP:0011366","MP:0006108","MP:0003613","MP:0003826","MP:0003827","MP:0004727","MP:0002174","MP:0000880","MP:0003558","MP:0004066","MP:0008487","MP:0011354","MP:0000830","MP:0000853","MP:0000852","MP:0002626","MP:0003672","MP:0003984","MP:0000538","MP:0000787","MP:0003557","MP:0001726","MP:0003446","MP:0000534","MP:0002230","MP:0002966","MP:0010982","MP:0001121","MP:0000520","MP:0000519","MP:0000955","MP:0012087","MP:0003604","MP:0002135","MP:0011290","MP:0002151","MP:0002152","MP:0001145","MP:0001119","MP:0003578","MP:0002989","MP:0000432","MP:0000433","MP:0004557","MP:0004559","MP:0004505","MP:0012685","MP:0009579","MP:0009718","MP:0003085","MP:0005221","MP:0004017","MP:0004180","MP:0002169","MP:0004936","MP:0002961","MP:0011365","MP:0011108","MP:0011087","MP:0011089","MP:0000527","MP:0006426","MP:0006425","MP:0009074","MP:0009076","MP:0009075","MP:0011292","MP:0002084","MP:0012176","MP:0012156","MP:0012136","MP:0012135","MP:0011098","MP:0003722","MP:0001701","MP:0001698","MP:0012276","MP:0000536","MP:0005644"]},{"id":"MGI:99783","label":"Lhx1","type":"gene","matches":[{"b":{"id":"MP:0000433","IC":4.054094985695492,"label":"microcephaly"},"a":{"id":"MP:0000433","IC":4.054094985695492,"label":"microcephaly"},"lcs":{"id":"MP:0000433","IC":4.054094985695492,"label":"microcephaly"}},{"b":{"id":"MP:0002966","IC":8.453940772660891,"label":"decreased circulating alkaline phosphatase level"},"a":{"id":"HP:0012594","IC":12.617865774103203,"label":"Microalbuminuria"},"lcs":{"id":"HP:0004364","IC":3.2599030098515027,"label":"Abnormality of nitrogen compound homeostasis"}}],"score":{"metric":"combinedScore","score":17,"rank":8},"taxon":{"id":"NCBITaxon:10090","label":"Mus musculus"},"id_list":["MP:0006032","MP:0011486","MP:0000913","MP:0006415","MP:0011366","MP:0006108","MP:0003613","MP:0003826","MP:0003827","MP:0004727","MP:0002174","MP:0000880","MP:0003558","MP:0004066","MP:0008487","MP:0011354","MP:0000830","MP:0000853","MP:0000852","MP:0002626","MP:0003672","MP:0003984","MP:0000538","MP:0000787","MP:0003557","MP:0001726","MP:0003446","MP:0000534","MP:0002230","MP:0002966","MP:0010982","MP:0001121","MP:0000520","MP:0000519","MP:0000955","MP:0012087","MP:0003604","MP:0002135","MP:0011290","MP:0002151","MP:0002152","MP:0001145","MP:0001119","MP:0003578","MP:0002989","MP:0000432","MP:0000433","MP:0004557","MP:0004559","MP:0004505","MP:0012685","MP:0009579","MP:0009718","MP:0003085","MP:0005221","MP:0004017","MP:0004180","MP:0002169","MP:0004936","MP:0002961","MP:0011365","MP:0011108","MP:0011087","MP:0011089","MP:0000527","MP:0006426","MP:0006425","MP:0009074","MP:0009076","MP:0009075","MP:0011292","MP:0002084","MP:0012176","MP:0012156","MP:0012136","MP:0012135","MP:0011098","MP:0003722","MP:0001701","MP:0001698","MP:0012276","MP:0000536","MP:0005644"]}],"resource":{"label":"OwlSim Server: http://owlsim.crbs.ucsd.edu/"},"a":{"label":"HP:0012594+MP:0000433","id_list":["HP:0012594","MP:0000433"]}}

capture

capture2

yuanzhou commented 8 years ago

I've added the data integrity check to see if metadata field if there. Otherwise show this error message instead of the actual phenogrid view with wrong color.

capture

harryhoch commented 8 years ago

Thanks for putting in error message, Zhou, but this is a bit cryptic. Why does this problem come up? Can we ensure that we have the right metadata?

yuanzhou commented 8 years ago

@harryhoch we don't have to worry about this with the regular simsearch results since all the required fields (a, b, metadata, resource) are always there and there's always matches. But the compare API used by the analyze phenotypes page has been unstable and for many queries (user-typed phenotypes and gene list) the resulting JSON doesn't contain b (all the matches info) or the metadata (contians maxICScore for creating the color scale) fields. I was struggling with those unexpected behaviors and have submitted several tickets to report this issue in monarch-app repo. I believe they are working on this.

I added the api check flags in the dataLoader and the actual data check for UI rendering in phenogrid.js solely to handle this compare API issue. So I can safely send the pull request to Kent and come back to remove those once they are addressed in the API level. Otherwise we'll prob lose track of this issue in the code.

harryhoch commented 8 years ago

ok, thanks. So long as they're working on this on monarch-app...

yuanzhou commented 8 years ago

I'll close this issue and add another issue for Exomiser hook.

monarch-initiative / phenogrid

Hooks -- owlSimFunction and geneList #203

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