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What is a COVID-19 relevant tool #506

Closed hansioan closed 7 months ago

hansioan commented 4 years ago

This issue is a placeholder for a discussion related to the bio.tools COVID-19 related tools list.

https://covid-19.bio.tools

What are the tools relevant to COVID-19?

How can we best keep a list of bio.tools entries related and relevant to COVID-19 without adding everything and creating a lot of noise?

Please feel free to tag anyone who would like to join the discussion.

Also related to #505

@bio-tools/core-dev @albangaignard @bgruening @joncison @frederikcoppens @mr-c @veitveit @magnuspalmblad @MigleSur @hhbj @hmenager @khillion @OlegZharkov @ValentinMarcon @matuskalas @inkuzmin @egonw @piotrgithub1 @annalenalamprecht @jvanheld @krab1k @smoe @ahtosalumets @thomasrosnet

tillea commented 4 years ago

Hi Hans,

On Wed, Mar 25, 2020 at 09:50:23AM -0700, Hans Ienasescu wrote:

How can we best keep a list of bio.tools entries related and relevant to COVID-19 without adding everything and creating a lot of noise?

I'm extremely interested into this question. Debian Med is creating an extra task which is currently populated also by cruft (which needs to be removed!) and lacking probably lots of relevant stuff: https://blends.debian.org/med/tasks/covid-19 I can easily extract relevant database fields with names and description of packages but I'm waiting for some input on this task first. The rough data list with some comments can be found here: https://salsa.debian.org/blends-team/med/-/blob/master/tasks/covid-19 Everything you find behind "Recommends" creates an entry. Any hint what to drop and what to add would be extremely helpful. Kind regards, Andreas.

hansioan commented 4 years ago

Hi Andreas,

I guess bio.tools and Debian Med are in a similar situation here. It would be super nice if we can work together and try to sync the packages/tools in both registries.

I am not sure what is relevant at this moment, initially I was thinking on some sort of covid-specific tools, for example I found this article: https://academic.oup.com/bioinformatics/advance-article/doi/10.1093/bioinformatics/btaa145/5766118 From the tool: "This tool is designed to use Blast and phylogenetic methods in order to identify the Coronavirus types and genotypes of a nucleotide sequence."

In this case one can say BLAST is a related tool, which in turn makes other aligners and sequence database searching tools also relevant.

What I thought initially was something a bit more specific to covid, like in the case of blast, they have the "Betacoronavirus Database": https://blast.ncbi.nlm.nih.gov/Blast.cgi?PAGE_TYPE=BlastSearch&PROG_DEF=blastn&BLAST_PROG_DEF=megaBlast&DATABASE=genomic/Viruses/Betacoronavirus

or the SARS-CoV-2 Sequences: https://www.ncbi.nlm.nih.gov/genbank/sars-cov-2-seqs/

So even very widely applicable tools like BLAST can be used specifically in the case of covid. Don't know if this works for all though.

hmenager commented 4 years ago

My 2 cents here:

On Wed, Mar 25, 2020 at 7:53 PM Hans Ienasescu notifications@github.com wrote:

Hi Andreas,

I guess bio.tools and Debian Med are in a similar situation here. It would be super nice if we can work together and try to sync the packages/tools in both registries.

I am not sure what is relevant at this moment, initially I was thinking on some sort of covid-specific tools, for example I found this article:

https://academic.oup.com/bioinformatics/advance-article/doi/10.1093/bioinformatics/btaa145/5766118 From the tool: "This tool is designed to use Blast and phylogenetic methods in order to identify the Coronavirus types and genotypes of a nucleotide sequence."

In this case one can say BLAST is a related tool, which in turn makes other aligners and sequence database searching tools also relevant.

What I thought initially was something a bit more specific to covid, like in the case of blast, they have the "Betacoronavirus Database":

https://blast.ncbi.nlm.nih.gov/Blast.cgi?PAGE_TYPE=BlastSearch&PROG_DEF=blastn&BLAST_PROG_DEF=megaBlast&DATABASE=genomic/Viruses/Betacoronavirus

or the SARS-CoV-2 Sequences: https://www.ncbi.nlm.nih.gov/genbank/sars-cov-2-seqs/

So even very widely applicable tools like BLAST can be used specifically in the case of covid. Don't know if this works for all though.

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bgruening commented 4 years ago

From a computational point of view, I don't think there is anything special in analyzing COVID-19 data, in respect to tools. The workflows we created are all using tools that have been used before for other scenarios. What about a little bit broader and trying to classify tools for "virology"? We could ensure EDAM ontologies for this and there are at least a few tools that are specific for analyzing virus genomes.

annalenalamprecht commented 4 years ago

Agreeing with @hmenager and @bgruening.

My first thought was: "Cool, if we would have a sort of Covid-19 tag in bio.tools, we could use that to create a set of tools for automatically creating Covid-19 workflows with APE". But then indeed, the range of computational problems around the pandemic is super diverse, and many of the general bioinformatics tools will be applicable. So sharing and documenting what HAS been used together for such purposes (workflows, methods sections...) seems to make more sense.

frederikcoppens commented 4 years ago

Full agree, tagging such a diverse set of tools with covid renders it largely useless. Virology sounds like a good idea for rather dedicated tools (generic blast is not in there IMO)

If you’re going over method sections and especially workflows: could we list these somewhere (google sheet or so is fine), then we can look to add these to WorkflowHub

F

On 26 Mar 2020, at 09:15, Anna-Lena Lamprecht notifications@github.com wrote:

Agreeing with @hmenager https://github.com/hmenager and @bgruening https://github.com/bgruening.

My first thought was: "Cool, if we would have a sort of Covid-19 tag in bio.tools, we could use that to create a set of tools for automatically creating Covid-19 workflows with APE". But then indeed, the range of computational problems around the pandemic is super diverse, and many of the general bioinformatics tools will be applicable. So sharing and documenting what HAS been used together for such purposes (workflows, methods sections...) seems to make more sense.

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub https://github.com/bio-tools/biotoolsRegistry/issues/506#issuecomment-604290491, or unsubscribe https://github.com/notifications/unsubscribe-auth/ACWFCM4ZZDJNYVE23L7RML3RJMFIPANCNFSM4LTTAZKA.

Frederik Coppens - Project leader & IT manager Head of Node ELIXIR Belgium Applied Bioinformatics And Biostatistics I.T. Support VIB-UGent Center for Plant Systems Biology Ghent University Technologiepark 71 - 9052 Ghent - Belgium Tel. +32(0)9 331 38 12 www.psb.ugent.be http://www.psb.ugent.be/

joncison commented 4 years ago

Hi folks

A few relevant searches:

EDAM Operation Virulence prediction: https://bio.tools/t?page=1&operation=%27Virulence%20prediction%27&sort=score

EDAM Operation Virtual screening (just one tool) https://bio.tools/t?page=1&operation=%27Virtual%20screening%27&sort=score

EDAM Topic Virology https://bio.tools/t?page=1&topic=%27Virology%27&sort=score

It could be good @hansioan to add a section on the splash page with (links to results for) key relevant EDAM concepts.

I'll compile a bigger list ASAP. Cheers !

hansioan commented 4 years ago

@joncison This search https://bio.tools/t?page=1&topic=%27Virology%27&sort=score

returns tools such as:

tillea commented 4 years ago

On Thu, Mar 26, 2020 at 06:36:56AM -0700, Jon Ison wrote:

I'll compile a bigger list ASAP.

That would be really cool. I'd adapt the covid-19 task of Debian Med[1] to your list since I'm very sure that it currently is missing relevant stuff as well as containing some useless stuff.

Its fun to work together with you guys, Andreas.

[1] https://blends.debian.org/med/tasks/covid-19

joncison commented 4 years ago

Hey folks

Here's some more relevant EDAM concepts (with links to bio.tools, this could inform a curation effort? There's also some relevant concepts I need to add to EDAM (see below). I'll keep on updating this post as I find more.

[1] NB. low transmembrane helix number is a key criteria for selection of vaccine candidates.

To add to EDAM: Please request new concepts directly in EDAM GitHub tracker (one concept / issue)

tillea commented 4 years ago

Hi Jon,

is there any way to map these ontology data to a list of software packages?

Kind regards

    Andreas.

On Sun, Mar 29, 2020 at 12:43:58PM -0700, Jon Ison wrote:

Hey folks

Here's some more relevant EDAM concepts (with links to bio.tools, this could inform a curation effort? There's also some relevant concepts I need to add to EDAM (see below). I'll keep on updating this post as I find more.

Side chain modelling (EDAM Operation) bio.tools search

Backbone modelling bio.tools search

To add to EDAM:

  • Antibody repertoire analysis (EDAM Operation)
  • as kids of Side chain modelling:
    • Antibody optimisation (optimize the antibody-interacting surface of the antigen (epitope))
    • Antigen optimisation (optimize the antigen-interacting surface of the antibody (paratope))
    • Antigen resurfacing (resurface the antigen by varying the sequence of non-epitope regions)
  • Epitope scaffold design (EDAM Operation) as kid of Backbone modelling with kids:
    • Scaffold search
    • Epitope grafting
    • Design optimization
  • Scaffold selection
joncison commented 4 years ago

Well, we have edamMap which maps text of all sorts (including publications, web pages etc.) to EDAM concepts. So this could be applicable?

hansioan commented 4 years ago

@tillea Would you like the list of tools that result from the searches @joncison wrote above or was your question regarding Debian Med packages?

joncison commented 4 years ago

@tillea @hansioan @hmenager @bgruening @annalenalamprecht @magnuspalmblad @veitveit @frederikcoppens @matuskalas @jvanheld

I'm composing a list of EDAM concepts relevant to vaccine design, virology etc. to include in EDAM 1.25 which will be released ASAP. It will include terms in above thread, but others. If you want to help out, please request new terms (or help define existing ones) by raising new issues or commenting on existing ones. Once I've exhausted my search (of the relevant literature) I'll write back on this thread in summary of the results. Thanks a million!

hansioan commented 4 years ago

@tillea if it's the bio.tools entry you needed, I added them to the attached file below. There are over 500 tools in all the searches above, but can't say how many are actually relevant.

issue_506_edam_tools.txt

joncison commented 4 years ago

hey @hansioan ... I think already with the terms above, we have enough for a new section on the bio.tools splash page. I'll keep on working at it ... but could be good to knock something up already ? I appreciate it's a bit of a rag-tag collection of concepts, but something is better than nothing.

hansioan commented 4 years ago

@joncison I already started adding to the https://covid-19.bio.tools subdomain, will look at these tools and see if I can find something I can add. I am in no way an expert on this, so I'm just adding something if it's obvious. What I can do is suggest these searches above, but even that doesn't mean they are that useful.

tillea commented 4 years ago

Hi Hans,

On Mon, Mar 30, 2020 at 02:48:03AM -0700, Hans Ienasescu wrote:

@tillea if it's the bio.tools entry you needed, I added them to the attached file below. There are over 500 tools in all the searches above, but can't say how many are actually relevant.

issue_506_edam_tools.txt

This looks like an exhaustive list. From reading it so far I do not see much that is familiar what we have inside Debian. I guess I need to wait until that list can will updated or wait for a priorisation what should be packaged next for Debian (if this is helpful in any way).

Thanks a lot anyway, Andreas.

smoe commented 4 years ago

On 30.03.20 14:57, Andreas Tille wrote:

Hi Hans,

On Mon, Mar 30, 2020 at 02:48:03AM -0700, Hans Ienasescu wrote:

@tillea if it's the bio.tools entry you needed, I added them to the attached file below. There are over 500 tools in all the searches above, but can't say how many are actually relevant.

issue_506_edam_tools.txt

This looks like an exhaustive list. From reading it so far I do not see much that is familiar what we have inside Debian. I guess I need to wait until that list can will updated or wait for a priorisation what should be packaged next for Debian (if this is helpful in any way).

Thanks a lot anyway, Andreas.

Also many thanks from my side. We can of course add a few of these that may have a free license and that are no website, but if we don't focus on a workflow then this is close to pointless, IMHO.

For mapping the tools in Debian to bio.tools/EDAM we have the metadata/edam) files. We could consequently rearrange our task page towards something more tree-like that reflects the EDAM ontology. And if we then even had threads through there that would link those tools that are used together in the same publication - yummy!

Steffen

hansioan commented 4 years ago

@tillea I agree that this list is a bit too big, but again it could be a starting point. Also as @smoe said workflows and publications are also a good starting point. So perhaps relevant tools can be:

I would also include here tools that have referenced covid-19 on their homepages/github . For example:

It would also be useful to keep an eye on websites that might come up with some covid-19 related workflows and software, I found some:

tillea commented 4 years ago

On Mon, Mar 30, 2020 at 02:33:29AM -0700, Hans Ienasescu wrote:

@tillea Would you like the list of tools that result from the searches @joncison wrote above or was your question regarding Debian Med packages?

Yes, that's exactly what I'm seeking for. I want to maintain a covid-19 task file which basically contains

Recommends: DebianBinaryPackage

entries. This is automatically rendered into a web page. I need a list of such binary packages (I'd volunteer to translate software names / source package names into binary packages) and feed this into the task file). We can then use our tool set - also give back to biotools for instance with an UDD query which I previously suggested (feel free to try this script if you are not aware of this). Kind regards, Andreas.