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  • #16
    Hi Dan et al

    I can likely help as well, but a couple things:
    The classification definitely makes sense, but I reckon it would also be helpful to have everything in one table so it can be copied out.

    Also some of the genomes are really -well sequenced- but far from being assembled in any useful way.
    So potentially one would not even only include a quality column but potentially even N50 if assembled?
    (And would this reflect only published genomes? We have Solanum pennellii assembled to an N50 of above 1Mbase, also the beta vulgaris genome is pretty complete)

    I would probably do the Solanacae and can provide some insight there.

    Cheers,
    björn

    Comment


    • #17
      The original intention of the page was 'public and published', but I've relaxed it a bit to include some currently unpublished genomes (annotated with the year "2013?") and even a couple where the assembly isn't even public yet (private communication)...

      You're right, we should annotate this clearly. At the very least I'm planning to add an 'ENA/BioProject' column with links to genome assemblies / bioprojects to make it absolutely clear when the assembly is public property.

      Adding assembly methods and statistics (and version) would be great too...

      About building one big table... Can we just cram the headers into the table design? Or should we have multiple classification columns? Whatever works I guess?

      I'm starting to get 'not-on-my-wiki' syndrome and feel the desire to pull this into SEQwiki for ultimate control, but having it on WP is the most visible, and will hopefully keep the page most up to date. Later we can publish it as a review in PLoS ;-)

      Cheers,
      Homepage: Dan Bolser
      MetaBase the database of biological databases.

      Comment


      • #18
        Also... anyone good with WikiData? We could put all figures in there:
        Homepage: Dan Bolser
        MetaBase the database of biological databases.

        Comment


        • #19
          Originally posted by dan View Post
          I'm starting to get 'not-on-my-wiki' syndrome and feel the desire to pull this into SEQwiki for ultimate control, but having it on WP is the most visible, and will hopefully keep the page most up to date. Later we can publish it as a review in PLoS ;-)
          How about adapting the SEQanswers/SEQwiki model by linking comments and discussion on the WP data back to SEQanswers forum?

          Comment


          • #20
            Originally posted by jimmybee View Post
            Absolutely. I'll populate some info tonight
            Column added... Fire away my friend!
            Homepage: Dan Bolser
            MetaBase the database of biological databases.

            Comment


            • #21
              Originally posted by Joann View Post
              How about adapting the SEQanswers/SEQwiki model by linking comments and discussion on the WP data back to SEQanswers forum?
              I'm not sure how the WP'dians would feel about that... You can ask them here:
              Homepage: Dan Bolser
              MetaBase the database of biological databases.

              Comment


              • #22
                I'm surprised nobody here mentioned Phytozome http://www.phytozome.net/

                Comment


                • #23
                  Originally posted by chadn737 View Post
                  I'm surprised nobody here mentioned Phytozome http://www.phytozome.net/
                  Thanks for the reminder. There's a lot there that are missing actually! I was working through the list but it's slow going... Getting there though!


                  Cheers,
                  Homepage: Dan Bolser
                  MetaBase the database of biological databases.

                  Comment


                  • #24
                    Thanks, sure I will go ahead.

                    Comment


                    • #25
                      Please feel free to start work at any time ;-)
                      Homepage: Dan Bolser
                      MetaBase the database of biological databases.

                      Comment


                      • #26
                        on it now
                        I have added different metrics for the completeness, maybe it is worthwile to split them up columnwise. well see for yourself
                        (apple/papaya/cucumber)

                        next corn/ricinus/solanace/peach

                        Cheers
                        b

                        Comment


                        • #27
                          Hi Dan

                          considering how much work (unsolvable CAPTCHAS) it is to put a reference it Wikipedia, maybe it is really worth considering to move this to the trusted SeqanswersWIKI site?

                          Best Wishes,
                          Björn

                          Comment


                          • #28
                            Originally posted by usad View Post
                            Hi Dan

                            considering how much work (unsolvable CAPTCHAS) it is to put a reference it Wikipedia, maybe it is really worth considering to move this to the trusted SeqanswersWIKI site?

                            Best Wishes,
                            Björn

                            Huge thanks for working on this Björn! Can you not just log in to WP to get round the captcha issue? Hmm... I see you have a user account... Do you still get this problem?

                            I see what you've been doing, collecting very detailed information about each assembly.... this is a huge amount of work! Thanks so much for what you've done here!

                            Instinctively, I think multiple columns are probably the way to go. It's a shame my (weak) efforts to get the MW developers to take SMW/SF seriously came to nothing, it would be great to be able to use forms to populate this data...

                            Is it worth looking at WikiData to help systematize this?


                            Many thanks again,
                            Dan.
                            Last edited by dan; 07-30-2013, 02:01 PM. Reason: I get confused between real and pseudo ;-)
                            Homepage: Dan Bolser
                            MetaBase the database of biological databases.

                            Comment


                            • #29
                              Hi Dan

                              I was logged in (this works flawlessly I never get logged out- thanks god) But maybe I don't have Wikipedia credibility yet.

                              I will simpley omit the references. Most are in anyway.

                              Cheers
                              Björn

                              Comment


                              • #30
                                Did a few edits today but will keep adding

                                Comment

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