dkNET-NURSA Challenge Kick-Off Webinar 04/27/2017

http://dknet.org #dkChallenge#dkChallenge
dkNET-NURSA Challenge
Kick-Off Webinar
Maryann Martone
Ko-Wei Lin
University of California San Diego
April 27, 2017
http://dknet.org

http://dknet.org #dkChallenge
Overview
● What is dkNET and why are we here?
● The challenge!
○ Why are we doing it?
○ The challenge task
○ Getting started
■ Sign up
■ How can dkNET help?
■ Other search tips

dkNET:NIDDK Information Network
A community resource and information portal
● An open community resource portal
● For basic and clinical investigators
● Provides seamless access to a collection of
diverse research and clinical databases:
○ Data
○ Materials
○ Tools
○ Funding opportunities
○ Literature
● Keep up to date with NIDDK related
opportunities and activities

dkNET-NURSA Challenge: Why are we doing it?
● It's a fun way to learn how to use dkNET and to learn some basics
about data search and curation
● Try a different approach to create and expand “big data for NIDDK”:
The impact of individual scientists working on small data are important!
● Introduction to NURSA (Nuclear Receptor Signaling Atlas,
https://nursa.org) and the Transcriptomine

Transcriptomine: Big data from small data
Fig. 1. Transcriptomine enables a cycle of data set discovery, reuse, and attribution to illuminate
uncharacterized biology of NR signaling pathways.
Becnel LB et al. Sci Signal. 2017 Apr 25;10(476)

dkNET-NURSA Challenge Task
Use dkNET to find and annotate as many discovery-scale (omics) data sets
as possible involving perturbations of nuclear receptor or coregulator
signaling pathways.
Required categories are:
1. Cistromic (ChIP-Seq)
2. Proteomic (mass-spec-based protein-protein interaction or
whole-proteome profiling)
3. Post-translatomic (phosphorylation, acetylation or other modification)
4. Metabolomic

Dataset Requirements
● Datasets must involve either:
a. Treatment with a small molecule perturbant (physiological ligand, drug,
synthetic organic compound, etc) of a nuclear receptor or coregulator;
OR
b. Genetic perturbation (knockout, knock-in, knockdown, overexpression) of
a nuclear receptor or coregulator.
● Datasets can be generated using cultured or primary cell lines or animal
models
See the NURSA website for a list of NR signaling pathways
and their corresponding small molecule & genetic perturbants
in the current version of Transcriptomine.

Win Prizes!
● $50 gift card will be awarded to the first 20 teams (individuals or groups)
who complete annotating five new datasets.
● Annotate as many datasets as you can to receive the opportunity to win a
bigger cash prize! A $500 cash prize, generously sponsored by SciCrunch
Inc., will be awarded to the team who accumulates the highest number of
points before the deadline.

Join the Challenge!
1. Get an account and sign up for the challenge
2. Start searching!
3. Submit datasets
4. Win prizes!
5. Invite your friends and colleagues

Register for the challenge
https://dknet.org Go to Challenge Page

Register for the challenge

Download the worksheet: curation required

Start searching
● dkNET basics
● Organization of dkNET
● Searching dkNET
● Challenge tips
● NR omics example
● Search tips

dkNET has 3 Primary Indices

dkNET Basic Structure
Search tip:
Start with general term
Use the facets and filters
to refine your search

Find a list of nuclear receptors

Find datasets

Other search tips: How do I compose a query?
Search Tips Description Examples
" " Use quotes around phrases that you want to
match exactly
"Polycystic kidney disease"
AND, OR Add AND between words will search for records
containing both terms; Add OR between words
will search for records with either term.
Diabetes AND obesity; Diabetes
OR obesity
- Negate a search term in the results Diabetes -NIDDK, will search for
diabetes but not the NIDDK
+ Require a search term in the results Diabetes +kidney
Use
autocomplete
Expand the search automatically with terms from
the ontology, e.g., synonyms, abbreviation
Use chronic kidney failure,
[disease] autocomplete feature,
the search will include chronic
kidney failure, CRF...etc.

Other search tips: My search returned too many
results, what should I do?
1. Select a category from the side panel that will only display
results in that category, e.g., select Type of Data -
Expression
2. Use Facets from the side panel to refine your search
3. If it seems to return a lot of irrelevant results, you can use
quotes around phrases you want to match exactly, e.g.,
"polycystic kidney disease" or remove query expansion.

Query expansion
You can also
remove
query
expansion if
it returns a lot
of irrelevant
results

Other search tips: My search returned zero or too
few results, what should I do?
1. Check if you are searching under "More Resources".
2. Use autocomplete vocabulary.
3. Remove symbols in the search terms, such as -, ()...etc., and spell out Greek
alphabet, such as alpha, beta...etc.
4. Check your search category. When you start a new search and would like to
get access to all resources instead of specific source, remember to either
click Community Resources or More Resources again. If you find there are
too few results, you might search under a specific category, subcategory, or
source from your last search.

Challenge FAQs Page

Scoring and Upload
● One point for each correct field in the attached Excel file, except Repository
Accession Number, which is worth two points
● If you search for a repository accession number or some other identifier but
do not find it, enter “Not deposited” in the Repository Accession Number
● For papers with multiple different omics datasets, enter these as separate
datasets - these will be scored as individual datasets
● Ten bonus points will be awarded for every multiple of ten reached in each
separate category
● Five bonus points will be awarded for every different NR signaling pathway
represented in the final list of datasets.
● Points will be awarded only for datasets not currently in NURSA (see
NURSA dataset directory)

dkNET BONUS POINTS!
● 4 bonus points will be awarded for utilization of dkNET during this challenge.
This includes finding datasets, repositories, funded awards, or articles to
identify datasets using dkNET.org (dkNET may be the starting point, but that
other tools may be used for the challenge).
● Provide dkNET URLs and record if you have found useful information to
receive 2 bonus points
● Write down your feedback from your experience using dkNET to find the
datasets to receive 2 bonus points

Upload the Worksheet

Hint: there are many other sources, e.g, grants
databases, the literature. The more you delve into
dkNET, the more creative you may become.
Always feel free to contact us with questions and we
are happy to help. #dkChallenge

Don't miss your chance to win gift cards and $500 cash.
Join the challenge now and submit ASAP!
● If you have questions or need tutorials
○ Contact info@dknet.org
○ Check out Challenge Page and FAQs
https://dknet.org/about/dknet-nursa-challenge
○ dkNET Help Page: https://dknet.org/about/help
● dkNET Introductory Webinar: May 10, 2017 11am PT
● Submission deadline: June 16, 2017 Midnight
● Invite your friends or colleagues
● Follow us @dknet_info #dkChallenge

dkNET-NURSA Challenge Kick-Off Webinar 04/27/2017

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dkNET-NURSA Challenge Kick-Off Webinar 04/27/2017