11 Responses

1. 

   Kawai Lee · January 17, 2017 at 19:15:41 · →

   Sorry, but the 4th link doesn’t work. -> https://youtu.be/ZNIQCrCIbL8

   Thx.

   1. 

      Arne Elofsson · January 17, 2017 at 21:03:20 · →

      Thanks for noting, should be fixed now.

   2. 

      Arne Elofsson · January 17, 2017 at 21:04:32 · →

      should work now

2. 

   Lorans · January 17, 2017 at 20:19:52 · →

   In the “Videos” section on this page, link nr 4 wont start since it is marked as a private clip. Could you please make it available for everyone?

   1. 

      Arne Elofsson · January 17, 2017 at 21:04:52 · →

      should work now

3. 

   Arne Elofsson · January 17, 2017 at 20:48:06 · →

   How do maintainers of biological databases go about when errors are
   detected in the database? Are erratic entries erased or are they kept
   but marked as invalid? I am thinking about protein IDs and such.

   What is the incitement for an experimental scientist to get data into
   a biological database? Does scientific journals require the author to
   upload experimental data to a biological database before the journal
   will publish the scientific paper?

4. 

   A · January 17, 2017 at 21:51:40 · →

   “Primary databases often hold only one type of specific data which is stored in their own archive “- specific data? like sequence specific? rather than structure or functional and vice versa ? or gene rather than proteins and vice versa.

   Is secondary database equivalent to derivative database? and the difference to primary is that it integrates primary, with additional information?

   Is interaction map anything more than just physical interaction? Or does it necessarily contain physical interaction information.

5. 

   Björn · January 18, 2017 at 06:04:53 · →

   What tools are used to evaluate the quality of e.g. nucleotide sequence data, expression data, gene annotations etc.?

6. 

   Björn · January 18, 2017 at 06:19:57 · →

   I just want to add one more biological database that is very useful for enzymes; BRENDA.

   http://www.brenda-enzymes.org/

7. 

   Javi Lanillos · January 18, 2017 at 09:05:09 · →

   Hello! I got a question about databases while playing a little bit with them:

   1a)
   I have been looking for the total number of existing biological databases (one never knows how many there are and which one to start looking at) in order to get an idea of what is available and if it is possible to figure out which ones should be better references.

   Here I attach the link where many of them are cited and arranged by fields and topics: http://www.oxfordjournals.org/our_journals/nar/database/c

   Thus, any suggestion how to start? Should we focus primarily in Uniprot and any other that will make us adapt better to this course? Should we take particularly into account those databases provided into this lessons sections (‘Databases that you should know something’)? I guess that once a researrcher/student gets more and more focused in one specific field, this great range of options narrows a bit mroe, right?

   1b)

   I made the comparison between string and Uniprot by using one of the examples that string provides: CDC15 Saccharomyces Cerevisiae

   http://string.embl.de/cgi/network.pl entry CDC15 (S.Cerevisiae)

   Then, for Uniprot, I typed:

   http://www.uniprot.org/uniprot/P27636

   So, it seems that with string I can get easily the website to see the 3D structure whereas uniprot provides me with a lot of annotated information like GO. Are these two examples focused differently so that we should know how each database is specialist on providing different views about a given protein?

   Thanks!

8. 

   Tianlin He · January 18, 2017 at 10:58:52 · →

   I am curious about how they calculated distance between individual spots in a interaction map.