[Bioc-devel] Identical methods in two packages
Laurent Gatto
lg390 at cam.ac.uk
Thu Sep 14 23:23:02 CEST 2017
On 14 September 2017 15:15, Hervé Pagès wrote:
> Hi,
>
> Note that right now the name of the Ontology getter matches the
> name of the corresponding field in all our annotations:
>
> > library(org.Hs.eg.db)
>
> > org.Hs.egGO[["92610"]][["GO:0005622"]]
> $GOID
> [1] "GO:0005622"
>
> $Evidence
> [1] "IEA"
>
> $Ontology
> [1] "CC"
>
> > library(GO.db)
>
> > GOTERM[["GO:0005622"]]
> GOID: GO:0005622
> Term: intracellular
> Ontology: CC
> Definition: The living contents of a cell; the matter contained within
> (but not including) the plasma membrane, usually taken to exclude
> large vacuoles and masses of secretory or ingested material. In
> eukaryotes it includes the nucleus and cytoplasm.
> Synonym: internal to cell
> Synonym: nucleocytoplasm
> Synonym: protoplasm
> Synonym: protoplast
>
> Also this name is consistent with what AmiGO is using:
>
> http://amigo.geneontology.org/amigo/term/GO:0005622
>
> So I actually don't think that we should rename the Ontology getter,
> sorry.
>
> @Laurent: any chance you use something else in rols?
Ontology,character is the constructor for the Ontology class, so it fits
quite well.
If I considered changing that constructor, I would also want to change
the name of the class (say something like OlsOntology) and all other
similar classes/constructor (Term, Properties, ...) to keep the naming
conventions withing the package consistent.
Here is how things are named in rols, according to the Ontology lookup
service (OLS): the ontology is GO, and CC, MF and BP are called
namespaces of that ontolgy. Wikipedia and the Gene Ontolfy site
(http://geneontology.org/page/ontology-documentation) also refer to them
as domains.
> go <- Ontology("GO")
> go
Ontology: Gene Ontology (go)
An ontology for describing the function of genes and gene products
Loaded: 2017-09-13 Updated: 2017-09-14 Version: 2017-09-12
49106 terms 67 properties 0 individuals
> got <- terms(go)
> got
Object of class 'Terms' with 49107 entries
From the GO ontology
GO:0005230, GO:0015276 ... GO:0032942, GO:0019987
> trm <- got[["GO:0005622"]]
> trm
A Term from the GO ontology: GO:0005622
Label: intracellular
The living contents of a cell; the matter contained within (but not
including) the plasma membrane, usually taken to exclude large vacuoles
and masses of secretory or ingested material. In eukaryotes it includes
the nucleus and cytoplasm.
> termOntology(trm)
[1] "go"
> termNamespace(trm)
[1] "cellular_component"
> table(unlist((termNamespace(got))))
biological_process cellular_component molecular_function
30596 4309 12132
This is how this work for all 198 ontologies available through the OLS.
I am going to leave things as they are for the moment (I anyway don't
have time now) and think a bit more about it.
Thanks anyway for considering doing changes in AnnotationDbi and for the
discussion.
Best wishes,
Laurent
> Thanks,
> H.
>
>
> On 09/12/2017 03:52 PM, Hervé Pagès wrote:
>> On 09/12/2017 01:58 PM, Vincent Carey wrote:
>>> For this particular problem, it may be worth noting that
>>>
>>> https://urldefense.proofpoint.com/v2/url?u=http-3A__geneontology.org_page_ontology-2Dstructure&d=DwIGaQ&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=ECJZN8XlNzgWTqEBbZjafknjX8AFaP25P-pVVk1_FnI&s=JGP585F0L1FCGBWgo2vmg1Tl4ieNB_z2HRGv0oEUVvk&e=
>>>
>>>
>>> describes CC, MF, BP as "sub-ontologies" of GO. AnnotationDbi might
>>> replace
>>> its Ontology() with subontology() to acquire those tokens.
>>
>> Thanks Vince for the suggestion. I like subontology() as a replacement
>> for Ontology() in AnnotationDbi.
>>
>> We'll make that change.
>>
>> H.
>>
>>>
>>> On Tue, Sep 12, 2017 at 4:28 PM, Michael Lawrence
>>> <lawrence.michael at gene.com
>>>> wrote:
>>>
>>>> I think I'm going to vote for the policy that methods with identical
>>>> signatures are currently unsupported by the methods package. It's
>>>> tough to imagine how they might work in any reliable and natural way,
>>>> and they totally break the methods package currently.
>>>>
>>>> In the grand scheme of things, generics should have constrained
>>>> semantics. If you guys can't reconcile the semantics, then you'll need
>>>> two different generics with the same name. But please think about the
>>>> users.
>>>>
>>>> Michael
>>>>
>>>>
>>>> On Tue, Sep 12, 2017 at 1:06 PM, Laurent Gatto <lg390 at cam.ac.uk> wrote:
>>>>>
>>>>> Hi Herve,
>>>>>
>>>>> I understand that there is a clash between the two identical methods.
>>>>> Both packages seem to have good reasons to implement their own
>>>>> `Ontology,character`. Such clashes are relatively frequent.
>>>>>
>>>>> My issue really is that when unloading AnnotationDbi's namespace,
>>>>> `Ontology,character` is removed from the methods' dispatch table, and
>>>>> thus becomes unavailable to rols users. What really should happen is
>>>>> that when AnnotationDbi's namespace is unloaded, the method in rols
>>>>> works again, similar to what happens for function.
>>>>>
>>>>> Is this something that is worth raising on R-devel?
>>>>>
>>>>> Best wishes,
>>>>>
>>>>> Laurent
>>>>>
>>>>> On 12 September 2017 16:35, Hervé Pagès wrote:
>>>>>
>>>>>> Hi Laurent,
>>>>>>
>>>>>> The 2 Ontology,character methods defined in AnnotationDbi and
>>>>>> rols do very different things. The 1st one expects a vector of
>>>>>> GO IDs and returns the GO sub-ontologies that they belong to:
>>>>>>
>>>>>> > Ontology(c("GO:0000009", "GO:0000012", "GO:0000006"))
>>>>>> GO:0000009 GO:0000012 GO:0000006
>>>>>> "MF" "BP" "MF"
>>>>>>
>>>>>> The 2nd one takes the name of an ontology and returns a
>>>>>> summary/description of it:
>>>>>>
>>>>>> > Ontology("efo")
>>>>>> Ontology: Experimental Factor Ontology (efo)
>>>>>> The Experimental Factor Ontology (EFO) provides a systematic
>>>>>> description of many experimental variables available in EBI
>>>> databases,
>>>>>> and for external projects such as the NHGRI GWAS catalogue. It
>>>> combines
>>>>>> parts of several biological ontologies, such as anatomy,
>>>>>> disease and
>>>>>> chemical compounds. The scope of EFO is to support the annotation,
>>>>>> analysis and visualization of data handled by many groups at
>>>>>> the EBI
>>>>>> and as the core ontology for OpenTargets.org
>>>>>> Loaded: 2017-08-16 Updated: 2017-09-12 Version: 2.87
>>>>>> 20063 terms 297 properties 0 individuals
>>>>>>
>>>>>> So the problem here is that even though now we have a single Ontology
>>>>>> generic in BiocGenerics for the 2 methods, we haven't really talked
>>>>>> about semantics i.e. what Ontology() is actually supposed to do.
>>>>>> Having
>>>>>> a generic without some sort of contract that methods are supposed to
>>>>>> honor is like having a generic called doSomething() and have people
>>>>>> start writing a bunch of methods for it ;-)
>>>>>>
>>>>>> The right thing to do here would be to use 2 different generics with
>>>>>> 2 different names e.g. Ontology() in AnnotationDbi and
>>>>>> ontologySummary()
>>>>>> in rols. Or GOontology() in AnnotationDbi and Ontology() in rols.
>>>>>>
>>>>>> If we want to keep the current situation and make it work properly, we
>>>>>> could implement the following hack: have rols depend on AnnotationDbi
>>>>>> and make the method in rols work on GO ids. The code would just need
>>>>>> to detect whether the strings in the supplied character vector start
>>>>>> with the "GO:" prefix and delegate to the code in AnnotationDbi (this
>>>>>> means that rols would need to be able to call that code so the body
>>>>>> of the AnnotationDbi method would need to be moved to an helper
>>>>>> function). An ugly hack though!
>>>>>>
>>>>>> What do you want to do?
>>>>>>
>>>>>> H.
>>>>>>
>>>>>> On 09/03/2017 07:59 AM, Laurent Gatto wrote:
>>>>>>>
>>>>>>> Dear all,
>>>>>>>
>>>>>>> This is a follow up to a previous email regarding the Ontology
>>>>>>> generic
>>>>>>> function, that is now in the BiocGenerics package. It seems that my
>>>>>>> problem was not only that both rols and AnnotationDbi defined the
>>>>>>> same
>>>>>>> generic, but they also both defined Ontology,character.
>>>>>>>
>>>>>>>> library("rols")
>>>>>>>
>>>>>>> This is 'rols' version 2.5.2
>>>>>>>
>>>>>>>> Ontology("go")
>>>>>>> Ontology: Gene Ontology (go)
>>>>>>> An ontology for describing the function of genes and gene
>>>>>>> products
>>>>>>> Loaded: 2017-08-31 Updated: 2017-09-01 Version: 2017-08-30
>>>>>>> 49075 terms 67 properties 0 individuals
>>>>>>>> Ontology
>>>>>>> standardGeneric for "Ontology" defined from package "BiocGenerics"
>>>>>>>
>>>>>>> function (object)
>>>>>>> standardGeneric("Ontology")
>>>>>>> <environment:0x2da7cf0>
>>>>>>> Methods may be defined for arguments: object
>>>>>>> Use showMethods("Ontology") for currently available ones.
>>>>>>>> showMethods("Ontology")
>>>>>>> Function: Ontology (package BiocGenerics)
>>>>>>> object="character"
>>>>>>> object="Ontology"
>>>>>>>
>>>>>>>> getMethod("Ontology", "character")
>>>>>>> Method Definition:
>>>>>>>
>>>>>>> function (object)
>>>>>>> {
>>>>>>> url <- ontologyUrl(object)
>>>>>>> x <- GET(url)
>>>>>>> stop_for_status(x)
>>>>>>> cx <- content(x)
>>>>>>> makeOntology(cx)
>>>>>>> }
>>>>>>> <environment:namespace:rols>
>>>>>>>
>>>>>>> Signatures:
>>>>>>> object
>>>>>>> target "character"
>>>>>>> defined "character"
>>>>>>>
>>>>>>> Until now, everything works as expected. The trouble begins when
>>>> loading
>>>>>>> AnnotationDbi.
>>>>>>>
>>>>>>>> suppressPackageStartupMessages(library("AnnotationDbi"))
>>>>>>>> showMethods("Ontology")
>>>>>>> Function: Ontology (package BiocGenerics)
>>>>>>> object="character"
>>>>>>> object="GOTerms"
>>>>>>> object="GOTermsAnnDbBimap"
>>>>>>> object="Ontology"
>>>>>>>
>>>>>>>> getMethod("Ontology", "character")
>>>>>>> Method Definition:
>>>>>>>
>>>>>>> function (object)
>>>>>>> .GOid2go_termField(object, "ontology")
>>>>>>> <environment:namespace:AnnotationDbi>
>>>>>>>
>>>>>>> Signatures:
>>>>>>> object
>>>>>>> target "character"
>>>>>>> defined "character"
>>>>>>>> Ontology("go")
>>>>>>> Loading required package: GO.db
>>>>>>>
>>>>>>> <NA>
>>>>>>> NA
>>>>>>>
>>>>>>> Ok, fair enough, these things happen. The issue is to recover
>>>>>>> Ontology,character from rols. If I unload AnnotationDbi's
>>>>>>> namespace (I
>>>>>>> also neet to unload GO.db, that got loaded automatically), there
>>>>>>> is no
>>>>>>> Ontology,character anymore.
>>>>>>>
>>>>>>>> unloadNamespace("GO.db")
>>>>>>>> unloadNamespace("AnnotationDbi")
>>>>>>>> showMethods("Ontology")
>>>>>>> Function: Ontology (package BiocGenerics)
>>>>>>> object="Ontology"
>>>>>>>
>>>>>>>> Ontology("go")
>>>>>>> Error in (function (classes, fdef, mtable) :
>>>>>>> unable to find an inherited method for function ‘Ontology’ for
>>>> signature ‘"character"’
>>>>>>>> rols::Ontology("go")
>>>>>>> Error in (function (classes, fdef, mtable) :
>>>>>>> unable to find an inherited method for function ‘Ontology’ for
>>>> signature ‘"character"’
>>>>>>>
>>>>>>>> getMethod("Ontology", "character")
>>>>>>> Error in getMethod("Ontology", "character") :
>>>>>>> no method found for function 'Ontology' and signature character
>>>>>>>> getMethod("Ontology", "character", where = "package:rols")
>>>>>>> Method Definition:
>>>>>>>
>>>>>>> function (object)
>>>>>>> {
>>>>>>> url <- ontologyUrl(object)
>>>>>>> x <- GET(url)
>>>>>>> stop_for_status(x)
>>>>>>> cx <- content(x)
>>>>>>> makeOntology(cx)
>>>>>>> }
>>>>>>> <environment:namespace:rols>
>>>>>>>
>>>>>>> Signatures:
>>>>>>> object
>>>>>>> target "character"
>>>>>>> defined "character"
>>>>>>>
>>>>>>>
>>>>>>> It is really the expected behaviour? How could I recover rols'
>>>>>>> Ontology,character?
>>>>>>>
>>>>>>> Thank you in advance.
>>>>>>>
>>>>>>> Best wishes,
>>>>>>>
>>>>>>> Laurent
>>>>>>>
>>>>>
>>>>>
>>>>> --
>>>>> Laurent Gatto | @lgatt0
>>>>> https://urldefense.proofpoint.com/v2/url?u=http-3A__cpu.sysbiol.cam.ac.uk_&d=DwIGaQ&c=eRAMFD45gAfqt84VtBcfhQ&r=BK7q3XeAvimeWdGbWY_wJYbW0WYiZvSXAJJKaaPhzWA&m=ECJZN8XlNzgWTqEBbZjafknjX8AFaP25P-pVVk1_FnI&s=8m_hDI6K7TnMToJXMG5Ud2QFHJfsppSA93X-dX5rne0&e=
>>>>>
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>>>>>
>>>>>
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>>>>>
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--
Laurent Gatto | @lgatt0
http://cpu.sysbiol.cam.ac.uk/
http://lgatto.github.io/
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