Submit HDO.db package

[huerqiang]

Update the following URL to point to the GitHub repository of the package you wish to submit to Bioconductor

• Repository: https://github.com/YuLab-SMU/HDO.db

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[bioc-issue-bot]

Hi @huerqiang

Thanks for submitting your package. We are taking a quick look at it and you will hear back from us soon.

The DESCRIPTION file for this package is:

Package: HDO.db
Type: Package
Title: A set of annotation maps describing the entire Human Disease Ontology
Version: 0.99.0
Authors@R: person(given = "Erqiang", family = "Hu", email = "13766876214@163.com", role  = c("aut", "cre"))
Description: A set of annotation maps describing the entire Human Disease 
    Ontology assembled using data from DO.
    Its annotation data comes from 
    https://github.com/DiseaseOntology/HumanDiseaseOntology/tree/main/src/ontology.
License: Artistic-2.0
BugReports: https://github.com/GuangchuangYu/HDO.db/issues
biocViews: AnnotationData, FunctionalAnnotation
Encoding: UTF-8
LazyData: false
RoxygenNote: 7.2.1
Depends:
    R (>= 4.1.0)
Imports: 
    AnnotationDbi,
    methods
Suggests: 
    rmarkdown,
    knitr,
    testthat (>= 3.0.0)
VignetteBuilder: knitr
Config/testthat/edition: 3

[vjcitn]

Thanks for submission, but please look at your compiled vignette. Vignette is not demonstrative. Should show some results like

> head(DOTERM)
         do_id                     Term
1 DOID:0001816             angiosarcoma
2 DOID:0002116                pterygium
3 DOID:0014667    disease of metabolism
4 DOID:0040001           shrimp allergy
5 DOID:0040002          aspirin allergy
6 DOID:0040003 benzylpenicillin allergy

You should also reflect some of the metadata in the vignette, such as the version of HDO.

[huerqiang]

@vjcitn Thanks. We have updated the vignette.

[vjcitn]

When I compile your package and look at vignette this is what I see:

please make this a document that a user will be able to learn from. It should start with a prose paragraph indicating your purpose in contributing the package to Bioconductor. It would be nice if it indicated the scientific value with a narrated example. It would also be appropriate to give a sense of the hierarchy perhaps with a screenshot like

[huerqiang]

@vjcitn Thank you for your suggestion, we have completed the relevant changes.

[huerqiang]

@vjcitn Hi, we have completed the revision for a few days, is it possible to proceed further? Please see if there are any other issues, thanks.

[vjcitn]

While I am passing this package, it is using obsolete methods.

> GO.db
GODb object:
| GOSOURCENAME: Gene Ontology
| GOSOURCEURL: http://current.geneontology.org/ontology/go-basic.obo
| GOSOURCEDATE: 2022-03-10
| Db type: GODb
| package: AnnotationDbi
| DBSCHEMA: GO_DB
| GOEGSOURCEDATE: 2022-Mar17
| GOEGSOURCENAME: Entrez Gene
| GOEGSOURCEURL: ftp://ftp.ncbi.nlm.nih.gov/gene/DATA
| DBSCHEMAVERSION: 2.1

Please see: help('select') for usage information
> HDO.db
Error: object 'HDO.db' not found
No suitable frames for recover()

The AnnotationDbi approaches are not used. The vignette uses as.list and toTable instead of select(). We need to update our contribution guidelines to ensure updated methods are used.

[vjcitn]

This is also somewhat confusing:

> DO.db::DO()
Quality control information for DO:

This package has the following mappings:

DOANCESTOR has 6569 mapped keys (of 11002 keys)
DOCHILDREN has 1811 mapped keys (of 2279 keys)
DOOBSOLETE has 2374 mapped keys (of 2374 keys)
DOOFFSPRING has 1811 mapped keys (of 2279 keys)
DOPARENTS has 6569 mapped keys (of 11003 keys)
DOTERM has 6570 mapped keys (of 11003 keys)

Additional Information about this package:

DB schema: DO_DB
DB schema version: 1.0
> HDO.db::DO()
Quality control information for DO:

This package has the following mappings:

DOANCESTOR has 66768 mapped keys (of 11002 keys)
DOCHILDREN has 11034 mapped keys (of 2279 keys)
DOOFFSPRING has 66768 mapped keys (of 2279 keys)
DOPARENTS has 11034 mapped keys (of 11003 keys)
DOTERM has 11003 mapped keys (of 11003 keys)

Additional Information about this package:

DB schema: DO_DB
DB schema version: 2.0

maybe use HDO()?

[huerqiang]

@vjcitn The HDO.db now support select() interface and we have changed DO() to HDO().

[huerqiang]

@vjcitn Hi, has this package entered the review process?

[vjcitn]

there is a sqlite file in your package exceeding size 5mb i am deliberating hiw to proceed need a few more days

[vjcitn]

I am sorry to be taking so long with this. You have done a good job of emulating the GO.db and using the AnnotationDbi methods. I am still conflicted with the question of how to handle ontologies in Bioconductor. https://obofoundry.org/ontology/doid.html shows that this resource is frequently updated. The "traditional annotation" package processing is not ideal, but maybe we should do this for now. It allows the >5MB file, right @lshep ? Let's go along this route if that works.

[lshep]

Yes. For a "traditional annotation" package that contains large files, the package can be reviewed here but the package will not be added to the git.bioconductor.org echosystem. The package will have to be manually uploaded by a team member any time there is an update to the package. The other alternative is to convert it to an annotationhub package and utilize that interface instead of having the large data file present in the package directly.

[huerqiang]

@lshep Hi, how is the review progress of this package, do I need to make any changes?

[bioc-issue-bot]

Your package has been accepted. It will be added to the Bioconductor nightly builds.

Thank you for contributing to Bioconductor!

Reviewers for Bioconductor packages are volunteers from the Bioconductor community. If you are interested in becoming a Bioconductor package reviewer, please see Reviewers Expectations.

[Kayla-Morrell]

@huerqiang - The package has been added to our devel builder and the script to make it available is currently running. It should finish in the next couple of hours and then the package will be available in the devel version of Bioconductor. Thank you for your contribution!