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biotoolsregistry : discovery portal for bioinformatics
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idconvert #77

Closed magnuspalmblad closed 7 years ago

magnuspalmblad commented 8 years ago

tool name:idconvert short description: A converter between pepXML and mzIdentML formats for peptide identifications from tandem mass spectrometry. Developed by the ProteoWizard team. URL:http://proteowizard.sourceforge.net/tools/idconvert.html topics: topic_0121|topic_0134 term: operation_0335 input format: format_3475|format_2332 output format: format_3475|format_2332 synonyms: none suggested parent:ProteoWizard license: Apache License V2.0

joncison commented 8 years ago

Sorry @magnuspalmblad I got cross-wires in email.

You can register this tool yourself directly in https://bio.tools/. Click the "log-in" (top-right) and create yourself a private account. Let use know (registry@elixir-dk.org) if you have problems.

magnuspalmblad commented 8 years ago

OK - my gmail account was not on the "whitelist", so I had to register with my LUMC e-mail account.

But I managed to add the tool and fill out most of the fields. However, I could not find pepXML in the list of formats, only mzIdentML. This means the annotation is currently incomplete!

veitveit commented 8 years ago

Strange, I found it here http://bioportal.bioontology.org/ontologies/EDAM/?p=classes&conceptid=http%3A%2F%2Fedamontology.org%2Fformat_3655 Maybe bio.tools did still not update to the newest EDAM release?

Generally, it would be sufficient for now to add the tool to Ms-utils. It will then be added to bio.tools together with all the other tools.

Cheers Veit On Mar 1, 2016 3:43 PM, "Magnus Palmblad" notifications@github.com wrote:

OK - my gmail account was not on the "whitelist", so I had to register with my LUMC e-mail account.

But I managed to add the tool and fill out most of the fields. However, I could not find pepXML in the list of formats, only mzIdentML. This means the annotation is currently incomplete!

— Reply to this email directly or view it on GitHub https://github.com/bio-tools/biotoolsregistry/issues/77#issuecomment-190747982 .

joncison commented 8 years ago

Please mail registry@elixir-dk.org asking to bump support of EDAM to 1.14. It will help to have "external" requests such as this to the list ... sorry this is cumbersome, bio.tools urgently needs fixing in this regard

magnuspalmblad commented 8 years ago

Dear All,

Regardless, it was a useful exercise for me to see how it works. When the new formats are there, I can use it as a practise for how to update a tool.

Cheers,

Magnus

From: veitveit [mailto:notifications@github.com] Sent: dinsdag 1 maart 2016 16:22 To: bio-tools/biotoolsregistry Cc: Palmblad, N.M. (CPM) Subject: Re: [biotoolsregistry] idconvert (#77)

Strange, I found it here http://bioportal.bioontology.org/ontologies/EDAM/?p=classes&conceptid=http%3A%2F%2Fedamontology.org%2Fformat_3655 Maybe bio.tools did still not update to the newest EDAM release?

Generally, it would be sufficient for now to add the tool to Ms-utils. It will then be added to bio.tools together with all the other tools.

Cheers Veit On Mar 1, 2016 3:43 PM, "Magnus Palmblad" notifications@github.com<mailto:notifications@github.com> wrote:

OK - my gmail account was not on the "whitelist", so I had to register with my LUMC e-mail account.

But I managed to add the tool and fill out most of the fields. However, I could not find pepXML in the list of formats, only mzIdentML. This means the annotation is currently incomplete!

— Reply to this email directly or view it on GitHub https://github.com/bio-tools/biotoolsregistry/issues/77#issuecomment-190747982 .

— Reply to this email directly or view it on GitHubhttps://github.com/bio-tools/biotoolsregistry/issues/77#issuecomment-190768610.

magnuspalmblad commented 8 years ago

OK, e-mailed registry@elixir-dk.org with this request.