Possibly missing association between pcr-product and expr-profile schema

[sibyl229]

Hi @mgrbyte,

I think there might be a schema translation issue going on here. According to ACeDB schema, there is an association between ?Expr_profile and ?PCR_product. Here is the relevant part in the model:

But in Datomic, I couldn't seem to find this association from either schema. I tried to query for any attribute with :pace/obj-ref namespace pcr-product or expr-profile, but none of the results appear related to this particular association.

[:find ?eid ?aid ?na
 :in $ ?na
 :where
 [_ :db.install/attribute ?e]
 [?e :db/ident ?eid]
 [?e :pace/obj-ref ?a]
 [?a :db/ident ?aid]
 [(namespace ?aid) ?na]
]

relates to WormBase/website#5070 on the microarray topography map discussion.

Thank you!

[khowe]

@mgrbyte looks like Expr_profile connection to PCR_product was commented out of the annotated models for WS248. Commit message does not say why though.

[mgrbyte]

@sibyl229 @khowe SMap constructs in ACeDB are not kept during the conversion process. Thomas re-implemented an intended equivalent to SMap in pseudoace, known as the "Locatables" API (See dialogue under the schema on that page for detail of the idea).

Anywhere you see SMap, look for the analogy using this locatables API. The following function shows how to traverse to a gene via CDS' from an expression profile. Note that a PCR product may reference many CDS', thus there may be many associated genes.

(defn gene-from-expr-profile
  [db expr-profile]
  (let [coding-seqs (-> expr-profile
                        ;; pcr-product via parent
                        :locatable/parent 
                        ;; cds holders via reverse relationship
                        :cds/_corresponding-pcr-product)
        corr-coding-seqs (map :gene.corresponding-cds/_cds coding-seqs)
        genes (flatten
               (for [cds corr-coding-seqs]
                 (map :gene/_corresponding-cds cds)))]
    (first genes)))

[mgrbyte]

@sibyl229 to get to the gene via the transcript, you'd need to use substitute the CDS based look-ups with Transcript ones if using the function above, i.e.:

:transcript/_corresponding-pcr-product instead of :cds/_corresponding-pcr-product

:gene.corresponding-transcript/_transcript instead of :gene.corresponding-cds/_cds

:gene/_corresponding-transcript instead of :gene/_corresponding-cds

[sibyl229]

Thanks a lot @mgrbyte . It works for me now. Closing!

[mgrbyte]

Just a note for posterity: the underscore notation for traversing relationships is only applicable when using the Datomic Entity API. In datalog queries, you can swap the position of variables applied to the canonical attribute to change the order of traversal, e.g:

..
: where
[?e :pcr-product/id ?pcr-product]
[?lp :locatable/parent ?e]]