New annotation R package (cellbaseR)

[melsiddieg]

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• Repository: https://github.com/melsiddieg/cellbaseR

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[bioc-issue-bot]

Hi @melsiddieg

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: cellbaseR
Type: Package
Date: 2016-04-17
Title: Querying annotation data from the high performance Cellbase web
    services
Version: 0.99.0
Author: Mohammed OE Abdallah
Maintainer: Mohammed OE Abdallah <melsiddieg@gmail.com>
Description: 
    This R package makes use of the exhaustive RESTful Web service API that has been
    implemented for the Cellabase database. It enable researchers to query and 
    obtain a wealth of biological information from a single database saving a lot 
    of time. Another benefit is that researchers can easily make  queries about 
    different biological topics and link all this information together as all 
    information is integrated.
License: Apache License (== 2.0)
Depends:
    R(>= 3.2)
Imports: 
    methods,
    jsonlite,
    httr,
    data.table,
    pbapply,
    tidyr,
    R.utils,
    Rsamtools,
    BiocParallel,
    Gviz,
    foreach,
    utils,
    parallel, doParallel
RoxygenNote: 5.0.1.9000
biocViews: Annotation
Lazy: TRUE
Collate:
    'commons.R'
    'AllClasses.R'
    'AllGenerics.R'
    'CellBaseParam-methods.R'
    'CellBaseR-methods.R'
    'cbAnnotateVcf-methods.R'
    'cbChromosomeInfoClient-methods.R'
    'cbClinicalClient-methods.R'
    'cbData-methods.R'
    'cbGeneClient-methods.R'
    'cbGet-methods.R'
    'cbProteinClient-methods.R'
    'cbRegionClient-methods.R'
    'cbSnpClient-methods.R'
    'cbSpeciesClient-methods.R'
    'cbTfbsClient-methods.R'
    'cbTranscriptClient-methods.R'
    'cbVariantClient-methods.R'
    'cbXrefClient-methods.R'
    'cellbase.R'
    'show-methods.R'
    'tools.R'
VignetteBuilder: knitr
Suggests:
    BiocStyle,
    knitr,
    rmarkdown

[bioc-issue-bot]

Your package has been approved for building. Your package is now submitted to our queue.

IMPORTANT: Please read the instructions for setting up a push hook on your repository, or further changes to your repository will NOT trigger a new build.

[lawremi]

Going to need a lot of work. Glad @hpages is on it.

I can't tell what these queries return, because the structure of the data.frame is undocumented. But I'm guessing they should be standard Bioconductor range objects, not data.frame. The API is confusing, because e.g. cbGeneClient() sounds like it is giving me a client for querying, but instead it is actually perfoming the query. Presumably this could use the TxDb API, at least for some queries.

[bioc-issue-bot]

Dear Package contributor,

This is the automated single package builder at bioconductor.org.

Your package has been built on Linux, Mac, and Windows.

On one or more platforms, the build results were: "ERROR". This may mean there is a problem with the package that you need to fix. Or it may mean that there is a problem with the build system itself.

Please see the following build report for more details:

http://bioconductor.org/spb_reports/cellbaseR_buildreport_20160923094257.html

[melsiddieg]

Dear Sir

I am Mohammed OE Abdallah, a visiting researcher at the computational biology lab at Cambridge university. I have developed an R package that serves as an R client to CellBase web services https://github.com/opencb/ cellbase ,which enable quick and easy access to heterogeneous biological information. CellBase takes full advantage of modern web technologies and is powered by high availability and high-Performance NoSQL database which results in almost real-time queries. Moreover, CellBase supports complex queries by integrating and linking together different biological sources. CellBase is currently used by many projects and institutions including;

• Genomics England (GEL) http://www.genomicsengland.co.uk/. Also known as the 100K genomes project
• The EMBL-EBI European Variation Archive (EVA) http://www.ebi.ac.uk/eva/?Home.
• The International Cancer Genome Consortium (ICGC) https://dcc.icgc.org/

and many others.

This R package makes use of the exhaustive RESTful Web service API that has been implemented for CellBase. It enables researchers to query and obtain a wealth of biological information from a single database saving a lot of time. Another benefit is that researchers can easily make queries about different biological topics and link all this information together as all information is integrated.

Currently, Homo sapiens, Mus musculus, and a total of forty-eight species are available and many others will be included soon. Results returned from the CellBase queries are parsed into R data.frames and other common R data structures so users can readily get into downstream analysis.

The R package is named cellbaseR and is available at https://github.com/melsiddieg/cellbaseR. I aim to make it available to broader R community through Bioconductor, as I think it will significantly simplify many annotations task in R, and is designed to be very straightforward and easy to use.

Best regards

Mohammed OE Abdallah

On Fri, Sep 23, 2016 at 4:40 PM, Michael Lawrence notifications@github.com wrote:

Going to need a lot of work. Glad @hpages https://github.com/hpages is on it.

I can't tell what these queries return, because the structure of the data.frame is undocumented. But I'm guessing they should be standard Bioconductor range objects, not data.frame. The API is confusing, because e.g. cbGeneClient() sounds like it is giving me a client for querying, but instead it is actually perfoming the query. Presumably this could use the TxDb API, at least for some queries.

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub https://github.com/Bioconductor/Contributions/issues/138#issuecomment-249196070, or mute the thread https://github.com/notifications/unsubscribe-auth/AIhzhmf9AcVGra_ar1lnSuPjUeYOtQ6sks5qs9begaJpZM4KE9Po .

[melsiddieg]

Dear Sir

This package is very similar in principle and functionality to BiomaRt package (Querying REST web services), only much faster, integrated, and versatile, that is also why it is very different from the regular R annotation packages as it does not query a local database. We opted for a data frame rather than genomic ranges as return value because not all the query results are range date, the R client also fetch annotation for transcription factors, clinical data, regulatory data, etc. a dataframe is more consistent and can be easily converted into genomic ranges when needed. I am fixing the issues right now, and hope to hear from you soon.

Best regards

Mohammed OE Abdallah

On Fri, Sep 23, 2016 at 5:15 PM, mohammed Elsiddieg melsiddieg@gmail.com wrote:

Dear Sir

I am Mohammed OE Abdallah, a visiting researcher at the computational biology lab at Cambridge university. I have developed an R package that serves as an R client to CellBase web services https://github.com/opencb/cellbase ,which enable quick and easy access to heterogeneous biological information. CellBase takes full advantage of modern web technologies and is powered by high availability and high-Performance NoSQL database which results in almost real-time queries. Moreover, CellBase supports complex queries by integrating and linking together different biological sources. CellBase is currently used by many projects and institutions including;

• Genomics England (GEL) http://www.genomicsengland.co.uk/. Also known as the 100K genomes project
• The EMBL-EBI European Variation Archive (EVA) http://www.ebi.ac.uk/eva/?Home.
• The International Cancer Genome Consortium (ICGC) https://dcc.icgc.org/

and many others.

This R package makes use of the exhaustive RESTful Web service API that has been implemented for CellBase. It enables researchers to query and obtain a wealth of biological information from a single database saving a lot of time. Another benefit is that researchers can easily make queries about different biological topics and link all this information together as all information is integrated.

Currently, Homo sapiens, Mus musculus, and a total of forty-eight species are available and many others will be included soon. Results returned from the CellBase queries are parsed into R data.frames and other common R data structures so users can readily get into downstream analysis.

The R package is named cellbaseR and is available at https://github.com/melsiddieg/cellbaseR. I aim to make it available to broader R community through Bioconductor, as I think it will significantly simplify many annotations task in R, and is designed to be very straightforward and easy to use.

Best regards

Mohammed OE Abdallah

On Fri, Sep 23, 2016 at 4:40 PM, Michael Lawrence < notifications@github.com> wrote:

Going to need a lot of work. Glad @hpages https://github.com/hpages is on it.

I can't tell what these queries return, because the structure of the data.frame is undocumented. But I'm guessing they should be standard Bioconductor range objects, not data.frame. The API is confusing, because e.g. cbGeneClient() sounds like it is giving me a client for querying, but instead it is actually perfoming the query. Presumably this could use the TxDb API, at least for some queries.

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub https://github.com/Bioconductor/Contributions/issues/138#issuecomment-249196070, or mute the thread https://github.com/notifications/unsubscribe-auth/AIhzhmf9AcVGra_ar1lnSuPjUeYOtQ6sks5qs9begaJpZM4KE9Po .

[bioc-issue-bot]

We only start builds when the Version field in the DESCRIPTION file is incremented. For example, by changing

Version: 0.99.0

to

Version 0.99.1

If you did not intend to start a build, you don't need to do anything. If you did want to start a build, increment the Version: field and try again.

[lawremi]

The low-level query interface could output a data.frame, I guess, but it would be nice to have high-level accessors, like genes(), that return the appropriate data structure, rather than expecting the user to do it.

Also, btw, if you used DataFrame you could call expand() instead of unnest() from tidyr and eliminate a dependency. I don't think data.table is needed there either.

It's not using BiocParallel correctly. For example, Annovcf() does not allow the user to pass down the BiocParallelParam object to control the parallelization. You probably should not depend explicitly on the foreach package.

The readIds() function reimplements VCF parsing. Please use VariantAnnotation::readVcf(). You could probably implement the existing VariantAnnotation API, e.g., predictCoding(), locateVariants(), using the web service, without introducing custom generics.

I'm not sure a web portal access package needs to implement any visualizations. If you returned appropriate data structures, the user could just pass them to GViz or whatever to make plots.

[melsiddieg]

We thought of implementing many convenience methods like snpByGene, variantByRegion, and so on, but we found that we need a lot of them to cover the functionality of the web services, so we chose a middle-way approach, however, we might implement some if you suggest that. The readIds function does not reimplement the vcf parser from the VariantAnnotation package as it merely reads and prepares the unparsed variants to be sent through GET for remote annotation in the CellBase server, in that regards it nicely complements the VariantAnnotation package by very fast (~ 1 minute for 10K variants) retrieval of a one-to-one corresponding data frame of comprehensive variants annotations without the forcing the user download any of the hefty annotations packages locally and doing the usual overlap based annotations, the CellBase server also enables phased annotations as well as structural variants annotations. You are right we could just prepare the gene model data and drop the Gviz dependency.

Best wishes

On Fri, Sep 23, 2016 at 8:36 PM, Michael Lawrence notifications@github.com wrote:

The low-level query interface could output a data.frame, I guess, but it would be nice to have high-level accessors, like genes(), that return the appropriate data structure, rather than expecting the user to do it.

Also, btw, if you used DataFrame you could call expand() instead of unnest() from tidyr and eliminate a dependency. I don't think data.table is needed there either.

It's not using BiocParallel correctly. For example, Annovcf() does not allow the user to pass down the BiocParallelParam object to control the parallelization. You probably should not depend explicitly on the foreach package.

The readIds() function reimplements VCF parsing. Please use VariantAnnotation::readVcf(). You could probably implement the existing VariantAnnotation API, e.g., predictCoding(), locateVariants(), using the web service, without introducing custom generics.

I'm not sure a web portal access package needs to implement any visualizations. If you returned appropriate data structures, the user could just pass them to GViz or whatever to make plots.

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub https://github.com/Bioconductor/Contributions/issues/138#issuecomment-249255362, or mute the thread https://github.com/notifications/unsubscribe-auth/AIhzhnq9mPaQLD6z2JoInMSScnpacNFcks5qtA40gaJpZM4KE9Po .

[lawremi]

It's calling things like strsplit() so that's parsing in my book. I think you users would very much prefer convenient ways to get the common data types (like gene annotations) into standard data structures.

[melsiddieg]

Let me clarify the readIds point, we are just preparing the reads for the REST call and none of it is parsed into R structures, only the response of the GET call is parsed into R data frames, On the other hand, the vcf parser from the VariantAnnotation reads the vcf file into an R data frame with all the added functionality, this does not serve our package in any way.

On Fri, Sep 23, 2016 at 9:08 PM, Michael Lawrence notifications@github.com wrote:

It's calling things like strsplit() so that's parsing in my book. I think you users would very much prefer convenient ways to get the common data types (like gene annotations) into standard data structures.

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub https://github.com/Bioconductor/Contributions/issues/138#issuecomment-249262915, or mute the thread https://github.com/notifications/unsubscribe-auth/AIhzhuekPV3qAEHSaotTaCPe_Kv4cJgeks5qtBWCgaJpZM4KE9Po .

[lawremi]

Please help me understand how calling scanTabix() and splitting on tab character is not reading the data into an R data structure. Sure, there's a ton of extra functionality in VariantAnnotation, but it's actually quite flexible, so you could disable most of the parsing (which happens in C instead of R) and probably get at least similar performance, with less work.

[melsiddieg]

Maybe I was not clear in my description, But my point is that none of the read variants is returned to the user, it is all preparing the variants in the specific way required by the CellBase server.

[bioc-issue-bot]

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[melsiddieg]

Hi

We have now reached the phase where my package is passing all R CMD checks in all three platforms without errors, warnings, or notes, and all Bioccheck without errors or warnings, however, I am getting this weird error:

\ checking loading without being on the library search path ... WARNING Error in loadNamespace(i, c(lib.loc, .libPaths()), versionCheck = vI[[i]]) :

How can I fix this?

Best regards

On Fri, Sep 23, 2016 at 8:36 PM, Michael Lawrence notifications@github.com wrote:

The low-level query interface could output a data.frame, I guess, but it would be nice to have high-level accessors, like genes(), that return the appropriate data structure, rather than expecting the user to do it.

Also, btw, if you used DataFrame you could call expand() instead of unnest() from tidyr and eliminate a dependency. I don't think data.table is needed there either.

It's not using BiocParallel correctly. For example, Annovcf() does not allow the user to pass down the BiocParallelParam object to control the parallelization. You probably should not depend explicitly on the foreach package.

The readIds() function reimplements VCF parsing. Please use VariantAnnotation::readVcf(). You could probably implement the existing VariantAnnotation API, e.g., predictCoding(), locateVariants(), using the web service, without introducing custom generics.

I'm not sure a web portal access package needs to implement any visualizations. If you returned appropriate data structures, the user could just pass them to GViz or whatever to make plots.

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub https://github.com/Bioconductor/Contributions/issues/138#issuecomment-249255362, or mute the thread https://github.com/notifications/unsubscribe-auth/AIhzhnq9mPaQLD6z2JoInMSScnpacNFcks5qtA40gaJpZM4KE9Po .

[lshep]

Please ignore this warning for now. This is an issue on our end that we are in the process of correcting.

[bioc-issue-bot]

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[hpages]

Hi Mohammed,

Thanks for submitting cellbaseR to Bioconductor. This sounds like a very promising package!

It has some serious usability issues though and some significant changes will be needed in order to address them. I'll start with the list below. I can't do more at the moment. Please address at your earliest convenience and I'll come back to this later.

Thanks, H.

1) There should be an effort to reduce dependencies. Right now library(cellbaseR) takes more than 20 sec on my laptop because it requires the loading of 80 packages via a namespace (as reported by sessionInfo())

2) All man pages use exactly the same text for \title and \description. For example, ?cbAnnotateVcf gives me this:

  cbAnnotateVcf,CellBaseR-method    package:cellbaseR    R Documentation

  This method is a convience method to annotate a vcf files. This methods
  is ideal for annotating small to medium sized vcf files.

  Description:

     This method is a convience method to annotate a vcf files. This
     methods is ideal for annotating small to medium sized vcf files.

This text seems like an appropriate description but is not suitable for a title. Title should fit in 1 line, be as short as possible, and not be made of several sentences.

3) Please add examples to man pages for cbAnnotateVcf and createGeneModel.

4) There is no need to wrap the returned data.frame into a CellBaseResponse object. Just return the data.frame and get rid of the CellBaseResponse class. I'm sorry if you've been told otherwise.

5) The "show" method for CellBaseR objects should print an \n at the very end of its output to bring the prompt (>) back to the beginning of the following line:

    > show(cb)
    An object of class CellBaseR
    | it holds the configuration for querying the Cellbase databases
    | to change the default species from human use CellBaseR(species='')> 

See the prompt at the end of the last line?

The "show" method for CellBaseParam objects has the same problem.

6) Why isn't the "show"method for CellBaseR objects displaying the current species?

    > cb2 <- CellBaseR(species='dodo')
    > cb2
    An object of class CellBaseR
    | it holds the configuration for querying the Cellbase databases
    | to change the default species from human use CellBaseR(species='')> 

Also the last line displayed suggests that the object is pointing at human which is not the case.

7) Is it expected that the species is not checked at construction time of the CellBaseR object?

8) The CellBaseR() constructor uses default values for some of its parameters (e.g. host="http://bioinfo.hpc.cam.ac.uk/cellbase/webservices/rest/", species="hsapiens"). It is considered good practice to formalize this in the interface of the CellBaseR() function itself by having the default values for these arguments explicitly set to what they really are (instead of NULL as it is right now).

9) As Michael pointed out, the naming of the cb*Client methods is confusing because totally unconventional. The widely used convention for such functions is to use something like getGenes (instead of cbGeneClient), getSnps (instead of cbSnpClient), etc... You absolutely don't need (and shouldn't) use the cb prefix for all your generics/methods. It would make sense to do so if these were ordinary functions but since they are generics, you shouldn't. That's actually the whole point of using generic functions.

10) No need to display BiocStyle version at the top of the vignette. Maybe you meant to display the version of the cellbaseR package instead?

[bioc-issue-bot]

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6e25975 removed CellBaseResponse class and its methods 172d16a Merge branch 'sep' into develop 9ea342d renaming all the methods to R/Bioconducctor friedl... c70ea18 Merge branch 'sep' into develop da65029 version bump 9c32f93 Merge branch 'sep' into develop

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[melsiddieg]

Dear package reviewers

As you can see we have pushed many updates to our package in the last few days to address the issues you raised. We made major changes to our package to make more user-friendly and more inline with the Bioconductor philosophy, These changes include: 1- Reducing the bloated dependency (improper import of Gviz), now the library loads in two seconds, and have only one third of the dependencies it used to have 2- Dropping the CellBaseResponse class, now the query results are returned directly to the user 3- Renaming all CellBaseR methods to R/ Bioconductor Friendly names 4- Added many convenience functions , getClinicalByRegion, getTranscriptByGen, etc 5- Added runnable examples to createGeneModel and AnnotateVcf 6- createGeneModel now only prepare the geneModel data and does not create a GeneRegionTrack 7- fixed the documentation, more updates are still to come

Your feedback is much appreciated Best regards

On Mon, Oct 3, 2016 at 2:30 PM, bioc-issue-bot notifications@github.com wrote:

Dear Package contributor,

This is the automated single package builder at bioconductor.org.

Your package has been built on Linux, Mac, and Windows.

Congratulations! The package built without errors or warnings on all platforms.

Please see the following build report for more details:

http://bioconductor.org/spb_reports/cellbaseR_buildreport_ 20161003073218.html

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[melsiddieg]

We also corrected the implemntation of the BiocParallel, now the BPPARAM=bpparam() is included in the function signature

On Mon, Oct 3, 2016 at 8:35 PM, mohammed Elsiddieg melsiddieg@gmail.com wrote:

Dear package reviewers

As you can see we have pushed many updates to our package in the last few days to address the issues you raised. We made major changes to our package to make more user-friendly and more inline with the Bioconductor philosophy, These changes include: 1- Reducing the bloated dependency (improper import of Gviz), now the library loads in two seconds, and have only one third of the dependencies it used to have 2- Dropping the CellBaseResponse class, now the query results are returned directly to the user 3- Renaming all CellBaseR methods to R/ Bioconductor Friendly names 4- Added many convenience functions , getClinicalByRegion, getTranscriptByGen, etc 5- Added runnable examples to createGeneModel and AnnotateVcf 6- createGeneModel now only prepare the geneModel data and does not create a GeneRegionTrack 7- fixed the documentation, more updates are still to come

Your feedback is much appreciated Best regards

On Mon, Oct 3, 2016 at 2:30 PM, bioc-issue-bot notifications@github.com wrote:

Dear Package contributor,

This is the automated single package builder at bioconductor.org.

Your package has been built on Linux, Mac, and Windows.

Congratulations! The package built without errors or warnings on all platforms.

Please see the following build report for more details:

http://bioconductor.org/spb_reports/cellbaseR_buildreport_20 161003073218.html

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub https://github.com/Bioconductor/Contributions/issues/138#issuecomment-251084248, or mute the thread https://github.com/notifications/unsubscribe-auth/AIhzhpxrb_fFEdp6vVJfsdhha5TgHqgoks5qwOdGgaJpZM4KE9Po .

[hpages]

Hi Mohammed, All these changes sound like great improvements. Will look at them ASAP (in the next 24h) and will let you know. Thanks! H.

[hpages]

Hi Mohammed,

I've been trying to access the cellbase webservice several times in the last 24 hours but I always get an HTTP error 404:

> library(cellbaseR)
> cb <- CellBaseR()
Error in open.connection(con, "rb") : HTTP error 404.

Is the service down? Any ETA for when the service will be available again?

Thanks, H.

[melsiddieg]

Hi

Yes, unfortunately, we will try to resolve this as fast as possible.

On Wed, Oct 12, 2016 at 1:41 PM, hpages notifications@github.com wrote:

Hi Mohammed,

I've been trying to access the cellbase webservice several times in the last 24 hours but I always get an HTTP error 404:

library(cellbaseR) cb <- CellBaseR() Error in open.connection(con, "rb") : HTTP error 404.

Is the service down? Any ETA for when the service will be available again?

Thanks, H.

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub https://github.com/Bioconductor/Contributions/issues/138#issuecomment-253179514, or mute the thread https://github.com/notifications/unsubscribe-auth/AIhzhp3FjV7Ens8VJVkhZR2h-XAihLZuks5qzLl1gaJpZM4KE9Po .

[bioc-issue-bot]

Received a valid push; starting a build. Commits are:

2a20017 fix host errors and version bump

[melsiddieg]

HI

We fixed that error, it turns out the CellBase version 4 server has been promoted to be the production server, Sorry for the inconvenience.

On Wed, Oct 12, 2016 at 1:41 PM, hpages notifications@github.com wrote:

Hi Mohammed,

I've been trying to access the cellbase webservice several times in the last 24 hours but I always get an HTTP error 404:

library(cellbaseR) cb <- CellBaseR() Error in open.connection(con, "rb") : HTTP error 404.

Is the service down? Any ETA for when the service will be available again?

Thanks, H.

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub https://github.com/Bioconductor/Contributions/issues/138#issuecomment-253179514, or mute the thread https://github.com/notifications/unsubscribe-auth/AIhzhp3FjV7Ens8VJVkhZR2h-XAihLZuks5qzLl1gaJpZM4KE9Po .

[bioc-issue-bot]

Dear Package contributor,

This is the automated single package builder at bioconductor.org.

Your package has been built on Linux, Mac, and Windows.

On one or more platforms, the build results were: "ERROR". This may mean there is a problem with the package that you need to fix. Or it may mean that there is a problem with the build system itself.

Please see the following build report for more details:

http://bioconductor.org/spb_reports/cellbaseR_buildreport_20161012112430.html