Proportal ReleaseNotes

Zero or null values

For the microarray experiments Nitrogen Limitation and Light Sensing, check if all of the genes have 0 in the mean(T) and mean(C) fields in each experiment. If they do, alter the mean(T) and mean(C) fields to read "NA" or some other entry indicating that there is no data for these fields.

Solution:

a. Set the mean(T) and mean(C) values in DB to be null if there is no measurement in the experiment;

b. Display the null value as "NA" on the page by modifying ${OCEAN}/templates/expression/probeset.html from,

    e.t_mean
    e.c_mean

to,

    e.t_mean| default_if_none:"NA"
    e.c_mean| default_if_none:"NA"

Verification:

   * http://proportal.mit.edu/probeset/MED4_ARR_1107_x_at/

Genbank ID

Link each Genbank ID on the Genome page for each genome to it's Genbank web page so users can download the genome if they are interested.

Solution:

Modify the page: ${OCEAN}/templates/genome/genome.html

   GenBank ID: <a class="external" href="http://www.ncbi.nlm.nih.gov/nucleotide/genome.gb_id">genome.gb_id</a>

To be done:

Another solution is to store the address in data_url table.

Verification:

   * http://proportal.mit.edu/genome/id=1/

Update publications

Update Publications for the following phage genomes to reflect Matt Sullivan's 2010 phage paper which described 16 phage genomes, SSM1, SSSM5, SSSM7, SSM2, SShM2, Syn1, Syn33, Syn19, Syn9, SPM2, PSSM7, PRSM4, PHM2, PHM1, PSSM4, PSSM2

   Genomic analysis of oceanic cyanobacterial myoviruses compared with T4-like myoviruses from   
   diverse hosts and environments. Sullivan MB, Huang KH, Ignacio-Espinoza JC, Berlin AM, 
   Kelly L, Weigele PR, DeFrancesco AS, Kern SE, Thompson LR, Young S, Yandava C, Fu R, 
   Krastins B, Chase M, Sarracino D, Osburne MS, Henn MR, Chisholm SW. Environ Microbiol. 2010 
   Nov;12(11):3035-56.

and Matt Henn's paper which describes phage genome sequencing, same phage genomes as above:

   Analysis of high-throughput sequencing and annotation strategies for phage genomes. Henn 
   MR, Sullivan MB, Stange-Thomann N, Osburne MS, Berlin AM, Kelly L, Yandava C, Kodira C, 
   Zeng Q, Weiand M, Sparrow T, Saif S, Giannoukos G, Young SK, Nusbaum C, Birren BW, Chisholm 
   SW. PLoS One. 2010

Solution:

a. Add both papers into data_publication table in DB using;

b. Link both papers with related projects/strains in data_projectpub table.

Verification:

   * http://proportal.mit.edu/genome/id=38/

External link

On the External Links page http://proportal.mit.edu/links/, add a link to

   VirMic website: http://www.cs.technion.ac.il/~itaish/VirMic/

Solution:

Add the link in ${OCEAN}/templates/basics/links.html

Verification:

   * http://proportal.mit.edu/links/

Correct mismatched host strain names

On the cyanophage genomes page: P-SSM4 host of isolation was Prochlorococcus NATL2A, not Prochlorococcus MED4.

The following mismatches are found by checking data_project and data_meta_data tables,

Mismatches

id	description	additional	host (on webpage)	Cyanophage Inventory	id2
25	P-SSM4	ProNATL2A	Prochlorococcus MED4	Prochlorococcus NATL2A	15
41	Syn19	SynWH8109	Synechococcus WH8019	Synecbococcus WH8109	35
43	Syn1	SynWH8101	Synechococcus WH8102	Synecbococcus WH8101	37
49	Syn5	SynWH8109	Synechococcus WH8019	SynWH8109	43
52	S-SSM4	SynWH8101	Synechococcus WH8018	Synechococcus WH8018	46
54	P-HP1	Prochlorococcus NATL2A	Prochlorococcus MED4	Prochlorococcus NATL2A	48

Solution:

All mismatches are corrected by following the confirmation in the Cyanophage Iventory spreadsheet.

verification:

   * http://proportal.mit.edu/project/cyanophage/

NCBI COGs

NCBI COGs need to be linked to their database entries.

Solution:

Modify ${PROPORTAL}/templates/protein/protein.embed.html from,

   NCBI COG: COG-tag

to,

   NCBI COG: <a class="external" href="http://www.ncbi.nlm.nih.gov/COG/grace/wiew.cgi?COGtag">COGtag</a> 

Modify ${PROPORTAL}/templates/protein/protein_list.embed.html from,

  COGtag 

to,

  <a class="external" href="http://www.ncbi.nlm.nih.gov/COG/grace/wiew.cgi?COG-tag">COGtag</a>

Verification:

   * http://proportal.mit.edu/protein/27641/0/
   * http://proportal.mit.edu/cluster/9407/

Title

On the microarray experiment pages, the table heading “ProCOG”, should read “CyCog”.

Solution:

It is defined in ${OCEAN}/templates/expression/gene_express_data_table_header.html. Simply chnage from "ProCOG" to "CyCog".

Verification:

   * http://proportal.mit.edu/gedata/exp=1&num=50&ig=0&q=10/

Probeset

ProbeSet IDs should also be searchable via the “Search Data” search box which appears on the homepage, the IDs look like this:

  MED4_ARR_0701_x_at, 

The page it would link to would be:

  http://proportal.mit.edu/probeset/MED4_ARR_0701_x_at/

Solution:

On hold. The search page is to be systematically modified for accurate search results.

Dataset download

From the NAR site, suggestions to submitters to the database issue: Do make data available for bulk download as flat files or relational database tables with associated documentation. We should at least make flat files (or db tables) of all called genes with cluster information available in both DNA and protein format.

Solution:

Datasets for previous publications have been available for download from the publication page.

Dataset upload

From the NAR site, suggestions to submitters to the database issue: Do allow users to provide feedback on your data and submit new data. Do respond to user feedback in a timely manner. We have the user feedback option, but submitting new data externally has not been done before. I am not sure if we should bring this up or not. It would be cool to incorporate other people’s data (especially if we are serious about making ProPortal more of a community resource) but also a lot of work. This is a topic for later discussion, but I just wanted to get it out there so we can think about it.

Solution:

On hold. Open for suggestions.

One possible solution is to set up a wiki type page for uploading.