1. The Refgene Database

2. Currently we use Google Spreadsheets to Track Reference Genes

3. Currently we use Google Spreadsheets to Track Reference Genes

4. Problems with Google Spreadsheets
Occasional errors picking a gene previously selected
Every group has their own Spreadsheet
Makes cross-access difficult
They are not integrated in any real way
They are hard to Maintain
Every month they are updated by hand
Hand editing leads to mistakes

5. It would be Easier to Have a Database to Keep Track of Reference Genes
Data from all reference genomes would be integrated and searchable
They could be automatically updated
New genes and their homologs in every species could populate automatically from Kara’s homology compute.
MODs could provide database reports to update stats on annotation progress
Stats for pubs and grant updates could be retrieved easily

6. Proposed Interfaces
Refgene interface: Used to set new target genes each month.
As genes are targeted, homologs are automatically populated from P-POD clusters
MOD interface: Used by MOD curators
Allows MOD curators to hand-modify individual records

7. Fields Required homolog gene identifiers for a MOD
Date that the gene was deemed comprehensively annotated
Date the gene was chosen as a reference gene

8. Functionality that should be on the Ref. Gen. Curation Home Page
Log in
Enter new curation target genes
Homologs: - Upload orthologs for those genes - Manually add orthologs - Enter 'curation status'
Generate reports

9. The Database Should also Accept Automated Loads from MODs
Curation status
Curation target genes
MOD ID
SGD
SGD
SGD

10. 1. Curator log in - 1 Curator Login To Curation Central
Once logged in, the curator name and MOD can be assumed anywhere that data is needed.
Also prevents random folks from editing and should probably also restrict editing capability to only homologs from the species you are a curator of?
We all still need to be able to add new target genes regardless of our MOD however.
Curator Login
To Curation Central
Login:
Password:
Login
Reference Genomes Snapshot
Target genes: 275
Species
Homologs
No homolog
Comprehensive
A.thaliana
220 10
190
C.elegans
200 30
189
D.rerio
175 35
170
D.discoideum
250 7
D.melanogaster
185 19
160
E.coli
100 25 98
G.gallus
120
H.sapiens
274 2
Etc… …
86%

11. Target Completion Date (MM-YYYY)
1. Curator log in - 2
Curation Targets
Logged in: doughowe | ZFIN
Gene Name
Completion target date
homologs
Report
[can edit]
View/enter homologs
View Curation Report
Upload New Targets
Target Completion Date (MM-YYYY)
Targets TAB file:
Browse
Upload
Upload orthologs
Select month:
pull-down list
Search Targets
[view all]
Gene Symbol Or
Entrez Gene ID:
Search result takes you to the homolog Add/Update page shown on the bottom of slide 13 for the specific target gene located in the search. More than one gene located by the search shows a list of these genes which then link to the homolog View/Add/Update page for each gene
Search
Reports:
TO DO List (not comprehensive)
ISS could be added
Potential outliers
View reports
by gene:
by organism:
Access to reports could be done a couple of ways
enter gene
Symbol or MOD ID
drop down list GO

12. 2. Upload New Targets - 1 Check that all required data is included
Check that no genes on new targets list have been a target or called as homologs previously…if so, reject load and alert curator to any/all duplications so they can select new targets and try again.

13. Target Completion Date (MM-YYYY) Upload Targets TAB file:
2. Upload New Targets - 2
Gene Name
MOD ID
Completion target date
[edit/autofill] (A)
[edit/autofill]
option 1
Upload New Targets
Target Completion Date (MM-YYYY)
Upload Targets TAB file:
Browse
option 2
Upload
Upload
Curator enters target date here; and that info is applied to the new table
load file
Gene Name
MOD ID
Completion target date
RNR1
SGD
CDC2
ADE4
POL6
MOD ID
SGD
SGD
SGD
Upload
(A) We need to be able to enter either an ID or a gene name (in the same or in a different column (B) Need a check for genes already selected

14. 2. Upload New Targets - 3 Your upload was successful!
Gene Name
MOD ID
Completion target date
RNR1
SGD
CDC2
ADE4
POL6
etc…
Upload
Your upload was successful!
Error: CDC2 (SGD ) has already been selected.
Please go back and replace this entry.

15. Target Completion Date (MM-YYYY)
3. Upload orthologs - 1
Logged in: doughowe | ZFIN
Upload New Targets
Target Completion Date (MM-YYYY)
Targets TAB file:
Browse
Upload
Upload orthologs
Select month: GO
pull-down list
Search Targets
[view all]
Gene Symbol Or
Entrez Gene ID:
Search
Reports:
TO DO List (not comprehensive)
ISS could be added
Potential outliers
View reports
by gene:
by organism:
enter gene
Symbol or MOD ID
drop down list GO

16. 3. Orthologs Upload orthologs
loads calculated data from P-POD and other available methods
Select month: GO
S. cerevisiae
E. coli
H. sapiens
D. discoideum
D. reiro
D. melanogaster
M. musculus
etc
RNR1|SGD
nrdA|P00832
RNR1|P34234
rnrA|DDB098908
rnra|DR23423
rnrA|DM8787
RNR1|MGI:2332
CDC2|SGD
no ortholog found
PK12
cdc22
ADE4|SGD
adeS|P32434
POL6|SGD
polR|P3434
etc…

17. Clicking View/Enter homologs goes to new Target gene-specific
Target Gene Symbol
Completion target date
Homologues
Report
POLA P09884
Aug 2006
View/enter homologs
View Curation Report
ADH1A P07327
Nov 2007
GOT1 P17174
Jan 2008
GOT2 P00505
Clicking View/Enter homologs
goes to new Target gene-specific
page to edit/add homologs
Homology Determination Methods
View/Enter/Edit Homolog page:
Target Gene: POLA (H.Sap)
Published homolog
Manual Analysis
HomoloGene
InParanoid
TreeFam
OrthoMCL
P-POD
Organism
Gene Symbol
Comprehensive curation (date)
Curator
D.mel
pol1a
1/20/2008
[Curator name]
[note]
D.rer
pola -
M.mus
No homolog
4/10/2007
C.ele
Species PD
curator enters symbol
curation date
curator name PD
[note]
This is an interface to support adding individual homologs to specific
target genes as well as edit previously added homologs..more detail next slide
Add

18. curator enters symbol/ID
Homology Determination Methods
View/Enter/Edit Homolog page:
Target Gene: POLA (H.Sap)
Published homolog
Manual Curation
HomoloGene
InParanoid
TreeFam
OrthoMCL
P-POD
Organism
Gene
Comprehensive curation (date)
Curator
Submit
curator enters symbol/ID
curation date
curator name
[note]
H. sapiens
C. elegans
D. Discoideum
D. melanogaster
E. Coli
M. musculus
r. norvegicus
S. pombe
Etc…
Curators enter gene symbols OR MOD object IDs. TAIR gene symbols are not unique.
pull down menu listing curators. If user login is supported, this column could probably be dropped and would be assumed behind the scenes based on the user login.
Currently logged in user displayed at top of page like this:
Logged In: dhowe|ZFIN.
A checkbox set to assert which homology determination methods were used to support the homology call. Full set may be more than shown here.
pull down menu OR organism already chosen based upon curator log in name
Clicking submit adds a new homolog to the DB after checking that the gene has not already been added as a target gene or homolog
Notes are used to describe anything specific about the orthology call

19. 4. Reports View curation report: POLA Options: select all/unselect all
Organism
Homologue
Date comprehensively curated
Arabidopsis thaliana
AT541
Caenorhabditis elegans
CE1121
Danio rerio
CD2121
CD2122
Dictyostelium discoideum
no homolog
Drosophila melanogaster
DM0022
Escherichia coli
Gallus gallus
GGAA11
Homo sapiens
P09884
Mus musculus
MGI:
Rattus norvegicus
RGD:
Saccharomyces cerevisiae
Schizosaccharomyces pombe
Options:
select all/unselect all
View annotations: * all * non-IEA * experimental √ √