Instruction of Gene CurationSeptember 8th, 2016

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Features • More than 10 gene information databases • Single or multiple choice of “Evidence, Inheritance, Penetrance, Age of

onset, PubMed” help to make decision• 8 status of curator easily know the progress of the curation• Filter button easily get the status of curation or well-baby or NICU baby• Set due date and email reminding of days prior or over due• Allow to re-assign gene-disease pair if curator is not available• Statistics of assignment for each curator in uploading help administrator to

know each curator’s assignments and progress easily• 5 status in administrator helps to monitor the progress of the curation• Statistic tables in Admin helps to know the count of reportable genes for

Well_baby and NICU_baby. • Filter button in curator easily get how many genes not started, curated,

need discussion and pending approval etc.• Export the current assignment in excel for both administrator and curator

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Login

first.last@mssm.edu

changeable

Select you “Curator”

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1 Link to criteria page 7 Triangle for sorting gene

2 Counts of each status 8 Triangle for sorting disease

3 Only export gene started 9 Triangle for sorting assignment date

4 Change password 10 Triangle for sorting due date

5 Logout 11 Triangle for sorting status . (Status is not clickable)

6 Change number of rows 12 Triangle for sorting action. (Link is clickable)

13 Search by gene or disease name

Due date email reminding: 2 days before, 1 day and 3 days after due date, a reminding email will send to you.

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Status & actionsStatus Meaning Action

New Newly assigned Start (remind starting curation)

Saved Assignment saved Edit (allow to revise)

Partnersaved

Partner saved assignment, but you not started yet Start (remind starting curation)

Discussion After both you and partner saved, ready for discussion Compare with partner(allow to revise after comparison)

Submitted Submit your curation after discussion Edit(allow to revise)

Partner submitted

Partner submitted after discussion, but you did not Discuss(allow to revise)

Pendingapproval

Waiting for administrator’s approval Browse(only browse, not allow to revise)

Approved Administrator approved your assignment Complete

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1 Gene information from ‘Resilience’ project

2 Orphanet disease and age of onset

3 Medicine in development for rare diseases by PHRMA .

4 10 out-sourced gene information, one click one link out.

5 If this gene in “New born screening”, it is yes

6 Disease information

7 Start curating

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All entries are mandatory. Most important is to always add inheritance pattern, penetrance, disease category, and PubMed first. You can save successfully only after finishing all.

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Simply click the round button or type within the yellow window as your choice .No empty yellow windows allowed before you clicking ‘Discussion’

Comparison curation with partner’s

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Tips for curator • Using the colorful filter to get newly assigned or

partner saved or pending approval gene quickly.• Input gene or disease in the “Search” to get gene

interested quickly• Sort the due date to know which gene should be

started earlier• ‘Export as CSV’ only export gene –disease pair start

curation(exclude ‘New’ and ‘Partner saved’). It is a good habit to backup your curation periodically (I suggested)

• Open the ‘Criteria’ link if you are not sure how to make decision

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•Administrator

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Administrator role and functions

• Uploading gene-disease pair• Assign gene-disease list to pair of curators• Set due date• Change or shift curators• Make finial decision• Export finial decision and curator’s decision • Monitor the progress of curation and behavior of

the curators

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1 Summary statistics 9 Logout

2 Gene-disease uploading 10 Well baby final decision

3 Not assigned gene list 11 NICU baby final decision

4 Assigned gene list & shift or change curator 12 Assignment date

5 Hide columns 13 Due date

6 Export finial decision by Admin 14 Status

7 Export decision by curators 15 Actions for each status

8 Export curation status 16 Search by gene or disease

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• Table 1 summarizes total number of gene-disease uploaded, assigned and in curation, pending approval and approved

• Table 2 summarizes the decision made by admin, and the total number of Well-baby reportable , NICU baby reportable genes.

Click the “Show Statistics” will show 2 tables, again, 2 tables gonne.

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• The first step of uploading is to check duplicates.• Only gene-disease pair delimited by ‘tab’ is allowed. The first column is gene, the second is disease.• Just copy the gene-disease pair from excel and then paste in the below blank area. • Example of input format is by clicking ‘Add example’ , 4 gene-disease pair will show up. • Then click ‘Duplicates check’.

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a. for example, click “Add example”, you will get 4 genes. Just take out one gene COA5, then click “Duplicate check”. Jump to b

b. 3 genes CLN6, CLN8 and COL11A2 are mismatched, you can continue uploading these 3 genes by clicking ‘UploadGene’. ‘Waiting for assignment’ will jump up see next page 16

Please see next page

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C1. Still using ‘Add example’ button to upload 4 genes CLN6,CLN8,COL11A2 and COA5 this time. Clicking ‘Duplicate check’, only one mismatched gene COA5 is left, which means 3 genes are duplicated from your input. Only one gene is qualified to upload.

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C2.If you want to know which genes are duplicated, press “Duplicates download” button, or if you want to know which genes are mismatched, clicking ‘Mismatched download’.

C3. After removing duplicates, then you can upload gene-disease pair by clicking “uploadGene’, and the ‘Waiting for assignment’ jump up and you can see the uploaded genes and start to assign

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f ed

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a Assignment statistics for each curator d Change the rows show up

b Select pair of curators e Check all rows if select the header circle, otherwise check one by one row

c Set due date f uploader

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4 Assigned gene, change or shift curators

Select curators and set due date, then check the genes which you want to shift or change curators, then select ‘ASSIGN’. The changed curators’ email will show up.

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Filters

• 3 filters for Well-baby,NICU baby and Status respectively. Check any grey circle, the gene under that category will show up, uncheck all grey circle, all the columns will show up. Allow multiple check.

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Other functions

• Decision making is same as curator• All the columns can be sorted except for 3

columns with filters• Export decision by admin or curator or status

with EntrezID• Search by gene and disease is to quickly find the

gene interested.

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