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planning for tool database?

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  • planning for tool database?


    I just wanted to know if there is any project with a team that it is involved in the improvement of the wiki software page?

    I think that it was more than a great idea to start that, and It would be a pity to stop here. It could ending up in the best and the DB-to-go to browse for any tool, check the popularity...and many others ideas I read in this forum.

    I read in other topic that there is a limitation of people with the knowledge to help on that. I don't know if this is the case for this page too.

    Anyway, I am willing to help if there is an active project for that, or help to recruit people to do that! I am sure there is plenty of people willing to help on that, the problem is to find them!


  • #2
    Hi lpantano!

    Thanks for your interest in the wiki! Very briefly, there are two main aspects to this project[1]:
    a) collecting and maintaining data, and
    b) building new pages and presenting data in new ways.

    Part a) is very active[2] and any help you can provide or recruit would be awesome! The more people working on the wiki, the closer we can come to the goals you mention above :-)

    Part b) is harder (requires more investment in learning the software), and essentially its all been done by me so far. However, there's tons of documentation[3], and anyone wanting to work on part b) is more than welcome!

    At some point I'm planning to write a database 'update' paper, and the main contributors will be listed as authors on that paper, as with the original[1].

    Thanks again for your interest!

    [1] For more details, see The SEQanswers wiki: a wiki database of tools for high-throughput sequencing analysis
    [2] Relative being the key word ;-) but see the page of recent changes to keep track of activity.
    Homepage: Dan Bolser
    MetaBase the database of biological databases.


    • #3

      thanks for the reply!

      I can be actively involved. I think that there is wonderfull information here.

      One thing that I don't know if there is information about how to fill the form when you create a new tool. I am talking about: bioinformatic method and biological domain although apply to the other tags. It could be possible to have some tips on what words to put here to try to remove redundacy?
      I think that if we get to reduce the redundancy we will increase the users and visits.

      1-I don't know if it would be possible to put something similar to select predefined tags, and maybe create new one in case there is no existing tags. Something like evernote does with notes. I know that maybe this is complicated and we can start just showing a text in red colour mentioning that "please try to use an existing tag used by other tools".

      2-Maybe we start also a call to all people who have the soft here to come back and update the information following some tips that will help to improve the DB.

      Really, I think that this is super important for the community, and I would like to help. Because I see this DB as the reference place to come to check how many tools you need to do you benchmark analysis, to know what options you have to analyze your data and to know if there is any free space to a new soft.

      what do you think about point 1 and 2?


      • #4
        Hi lpantano,

        Great news that you can be involved!

        I like both these ideas :-)

        Currently the form fields use 'auto completion' [1] to try to help users to use standard terms, but you are right, a lot of 'overlapping' terminology has been used... You can see all unique values here:
        As an aside, that page is a great place to start when working on data standardization. You can quickly see common vs. rare terms, and a few clicks take you to the pages to update.

        Additionally, we build a page for each term, which tries to integrate data from the EDAM biological software ontology [2]. So we could flag all terms that aren't formally in the ontology (and either work to rename them, or request them to be added in EDAM).
        As an aside, we clearly need to make EDAM integration more visible... I just build the pages and give up ;-)

        Here are some examples:
        * Biological domain -
        * Bioinfx method -

        On those pages the description text and synonyms are queried from EDAM via the BioPortal API [3]. It would be possible to have the form auto completion be keyed on that source rather than the terms used locally, but it's technically challenging to present the users with definitions wile auto completing (although I think that would be ideal).

        About point 2, I forget weather we collect contact email data for each tool? If not, I could add that field and then we could mail everyone on the list with a 'please check your data' shout... I think at least this would be a good way to get more logos uploaded... Again, the display of logos is something that can be improved a lot (I hate design!)

        Many thanks again for your interest in this project! I think cleaning data could be a great way to get your hands dirty to begin with.

        1. MediaWiki.Org/Extension:Semantic_Forms/Autocompletion
        2. http://EDAMOntology.Org (the "Biological domain" field on our site matches the EDAM 'topic' branch, while the "Bifx Method" field matches the EDAM 'operation' branch.
        3. Funnily enough, we're one of the biggest users of the BioPortal API! Here is a link to the EDAM widgets on BioPortal.
        Last edited by dan; 07-30-2013, 01:37 PM. Reason: Wanted the aside text to be small, not big!
        Homepage: Dan Bolser
        MetaBase the database of biological databases.


        • #5
          You can call me Lorena.

          Thanks for the information.

          It would be great to have all term that are not in EDAM, adn modigy those. How can we do that?
          Once I have those terms I can start changing each entry. What I don't know here is how to find the correct term in case it exists, and then how we can create otherwise? Once I have this information I will put my hands on it. I am willing to!

          Defenetly it would be great, although I don't know if possible as you say. But knowing that we can give this information to the user, we can put some tips like: "check first which term suit for you tool...blablabla" (probably some will do it).

          I think there is not input for email. It would be great. Meanwhile, could you have all users who have put any entry, get their emails and send them any message?

          I think that we can do:

          1-email to all users of the software wiki telling how to reduce redundancy
          2-a general post somewhere try to call more people to put more tools. We need just to post the message in the correct forums and I am sure we will be get a good reaction. SeqAnswer is famous enough to atrack people. Although I would do this after point 1 is done, the terms are minimized according to EDAM, and we have some tips to help new users.

          If you want I can start wirting a draft to send to the users, then you improve it , and send it. And this would help to write some tips for new users on how to choose the correct EDAM term.

          let me know what do you think!


          • #6
            Hey Lorena!

            One of the EDAM devs created a putative mapping between terms in SEQwiki and EDAM that i put here:

            You can visit any term to see if it has a successful lookup in EDAM (done via the BioPortal REST service), e.g.:
            * vs.

            You can search for terms and define your own mappings using the tools on the BioPortal for EDAM:

            In case of missing mappings, we can pester the authors.

            I really like your ideas for emailing, sorry I haven't added a contact field yet.

            Please don't think that you have to wait for me when working on SEQwiki! Really it's your project too. You can take the lead and be the lead author on the next publication!

            Homepage: Dan Bolser
            MetaBase the database of biological databases.


            • #7
              OK, I've added the email field and filled it in for about 5 tools:

              Please feel free to start work on the wiki any time :-)
              Homepage: Dan Bolser
              MetaBase the database of biological databases.


              • #8

                sorry about the silence. I have been travel during these two months and thinking how to get people involve in this.

                I have some ideas but one I think that could be done right now.

                any way to create a NEW page where tools are to explain about our new great project to improve the database. It would be similar to the wiki projects to improve page. If you create it, I can fill it with words and figure. My main idea is to explain how to help (just improving existing tools or adding new toolsaccording to EDAM classification) and why is so important.
                What do you think?

                My second effort would be to ask for a Special Sesion during ISMB2014. The idea is to be a couple of hours all people editing the wiki. It would be good to try if we at least get 10 people

                After that I will tell you about other ideas, but first I think it is important to have a page explaining this new initiative, so I can send emails with the link to all people I know

                let me know!



                • #9
                  Excellent suggestions! I agree 100%

                  Lets put this within the 'help' pages of the wiki. I've been very remiss on that front, as there is practically no user-help whatsoever! I think it's a really good idea to plug this gap with some clear guidelines for would-be contributors!

                  Your idea to have a session at ISMB is fantastic! If we could do that it would be awesome! What are the steps involved?

                  Thanks so much for helping with the wiki! I'm looking forward to new ideas, but as always, very short of time to do anything concrete...

                  Should we draft out the form of the help page to begin with? If you made an overview (i.e. things you'd like help with), I'd be able to fill in details... I think the 'Help' Namespace is the right place to put it...

                  Thanks for not giving up on this ;-)
                  Homepage: Dan Bolser
                  MetaBase the database of biological databases.


                  • #10

                    I will work in a draft and then send it to you. This way you can suggest/comment, this will help a lot.

                    About ISMB, we need to send a proposal by Nov 22. Again, I can start with a draft and then you can help as well. And if you think anybody who can be interested, ask him/her to join us

                    I will try to do it for the end of this week!

                    see you!


                    • #11
                      Draft it on the wiki, then anyone can edit!

                      Good luck
                      Homepage: Dan Bolser
                      MetaBase the database of biological databases.


                      • #12

                        I wrote down some tips to add/edit tools. They are on help pages.

                        I think that it would be good to have a link in red colour, or anything that catch attention on the following pages that I don't know how to add it:

                        2-at the top of the page when someone is adding the tool. The form page. Or next to the input field when you have to type the terms of your tool

                        what do you think?

                        Another ideas that could be done quickly.

                        1-we can create a specific place to discuss about the term used to classified the tools in the forum, maybe this way we can create a community to agree in terms, and in case that appears new methods, it would be easy to create a new term. If so, we can put this link on the same place I mentioned before.
                        2-if a list you some terms that should be change in many tools, could you do it automatically?. There are terms that are wrong in ten or more tools, and it is a little pain in the ass to change them one by one

                        more ideas, but best work on these first


                        • #13
                          Maybe it is not the real place to answer, but while on a project about creating a pipeline I found your Wiki Tool page and it was great but I found some related tools not listed there.
                          I would like to expand it in the Google Summer of Code but I don't know if some annotation tools are welcome to the software list. As it is not the main purpose of the community.
                          Any thoughts?


                          • #14
                            I don't think this approach will have a more productive model than the usual one.