ODDT beta-user guide-v0.9.12amc

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ODDT, user guide, latest version

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ODDT beta-user guide-v0.9.12amc

  1. 1. Open Drug Discovery Teams(ODDT)USER GUIDE and FAQs – Beta versionv0.9.12May 2013Dr. Sean EkinsCollaborations in Chemistry, A division of Collaborations in Communications, Inc.Dr. Alex M. ClarkMolecular Materials Informatics, Inc.Project DescriptionThe Open Drug Discovery Teams (ODDT) project provides a free iOS mobile app(https://itunes.apple.com/app/oddt/id517000016) primarily intended as a research topicaggregator of open science data integrated from various sources on the internet. Todate this has focussed on rare and neglected diseases as well as chemistry topics.SponsorshipCurrently the mobile app is sponsored by the Royal Society of Chemistry (RSC). Thecontent of the app is independent of this, and is consists entirely of open access articlesand data.Fig 1. About screen showing RSC sponsorship
  2. 2. User GuideThe entry screen to the app displays the topics ranked by use (Fig. 2).Fig 2. Entry screenTapping a topic image opens the topic browser, starting with the incoming page. Newlyadded content is listed on the right (Fig. 3).Can use multipleTwitter accounts usericonStats summaryAbout AppNews feedTopic panels
  3. 3. Fig 3. Incoming screenEach tweet that has been introduced into the data collection is considered to be adocument. A document can be endorsed or disapproved (Fig. 4),Fig 4. Endorsing or disaproving factoidsThe way things work presently is that new documents are added to the correspondingtopic headings, and if they get a positive endorsement, they stick around forever, unlessthey get voted back down. Documents with zero-or-less endorsements get removedafter a week, which means that the data collection loses all record of the entry. Thelatest version of ODDT records the number of new documents added to each topic perday, and coarse levels of summary information. These statistical aggregates areretained forever, which means that it is possible to track activity levels. Fig 3. shows anextra button in the bottom left corner (i) that is shown on the first page when viewing atopic. Pressing it brings up a statistics box (Fig 5) which could be useful for followingcontent.Click here to endorse ordisapproveClick here to preview articleIncoming data is sorted bytime of additionClick on image toopen it
  4. 4. .Fig 5. Statistics box for tuberculosis incomingThe hyperlinks to factoids can be followed. The recent page shows factoids with one ormore vote (Fig. 6).Fig 6. Recent screenThe content section shows the most popular voted content in rank order (Fig. 7).Recentfactoids with a votecount of +1 orbetter
  5. 5. Fig 7. Content screenMolecule thumbnails can be viewed by tapping on the link to view inline (Fig 8A) or thepreview panel can be tapped on to view the molecular data, as interpreted by the app(Fig 8B).AClick on image to openitRankedcontentContent is currentlyanything with a votecount of +1 orbetter, sorted bymost popular first
  6. 6. BFig 8. Viewing moleculesBack on the entry screen, tapping the statistics summary button opens a listing ofendorsements, disapprovals, injections and retirements for each hashtag (Fig. 9).Fig 9. EndorsementsThe appearance of the ODDT app on the iPhone (or iPod) is overall similar, with lessscreen space for showing topics (Fig. 10)
  7. 7. Fig 10. iPhone appearanceIntended use of AppTopicsThe selection of topics included in ODDT is driven by our interest in rare and neglecteddiseases as well as in various aspects of chemistry. To date we have the followingtopics covered: Tuberculosis, Malaria, Chagas disease, Leishmaniasis, HIV/AIDS,Huntingtons disease, Sanfilippo syndrome, Global Genes, Green Chemistry, Drugrepurposing, Giant Axonal Neuropathy, Hunter syndrome, Real time chemistry,Hereditary Neuropathy Foundation, H5N1, Rare Disease report, FibromuscularDysplasia, iCancer and ACS Chemical Information.All of these subjects have high potential for positively impacting the researchenvironment using computational approaches and dissemination information via mobileapps.We have defined a number of rare disease and chemistry related topics, correspondingto Twitter hashtags:#tuberculosis#malaria#hivaids#huntingtons#sanfilipposyndrome#leishmaniasis#chagas#rarediseases#h5n1#greenchemistry#hhf4gan#MPSII #huntersyndrome #hunterparents#realtimechem
  8. 8. #HNF#raredr#fmdaware#icancer#ACSCINFWhat can you do to use ODDT?Its simple:1. If you see an article of interest or want to say something about any of thesetopics then all you need to do is simply add the hashtag above. If you blog aboutany of these topics we should be able to capture them from the keywords above.2. If you want the document to be saved just add the hashtag #oddt – this causes atweet to "auto-endorse" itself when it is added to the topic.That’s it.ODDT is chemistry awareAs shown in Figs 7 & 8, ODDT handles molecule structures and enables them to beopened in MolSync or SAR Table. This enables ODDT to be used to create databasesof small molecules and associated data. You can use your imagination of how you couldcreate datasets for the diseases that interest you and view that data in ODDT.Where to next?As the software collection evolves and improves in its capabilities, data from openscience will be integrated and made usable within a common framework. Teammembers will be able to borrow and reuse a growing collection of existing data.Networking and collaboration features will be introduced, allowing researchers to postincomplete or speculative data, while other researchers fill in missing details, and thecommunity as a whole can debate, contest or endorse data based on its quality. ODDTmay also contribute to the nascent development of “nanopublications”. The app couldalso be used as a type of open lab notebook whereby individual researchers share links(URLs) to content and the app aggregates these.
  9. 9. While this system is nominally intended for annotation of content that is fully accessiblevia the original URL, it is potentially quite useful to annotate documents to which manyusers do not have access, e.g. articles that are behind a journal pay wall. The collectiveannotations of the users who have access to the article may provide enough informationto allow some users to gain insights that would otherwise only be accessible bypurchasing and reading the full article. It also has potential as a path to assemblearticles from scratch, in a fully open medium, and institute a kind of informal peerreview. In addition this functionality goes further towards an open notebook use casescenario in which the scientist publishes their results whenever a suitable point isreached, whether or not the results are sufficiently complete to warrant dissemination ina traditional peer reviewed article.NIH Data Sharing Plan – Why ODDT could be the solutionHelping collaborators with their NIH grants (R01, U19, SBIR, STTR, etc.), one is struckby something that has to be done early in most cases yet is usually left till last. That is ofcourse the DATA SHARING PLAN. To use the words from the NIH website(http://grants.nih.gov/grants/policy/data_sharing/data_sharing_guidance.htm):“In NIHs view, all data should be considered for data sharing. Data should be made aswidely and freely available as possible while safeguarding the privacy ofparticipants, and protecting confidential and proprietary data. To facilitate datasharing, investigators submitting a research application requesting $500,000 or more ofdirect costs in any single year to NIH on or after October 1, 2003 are expected toinclude a plan for sharing final research data for research purposes, or state why datasharing is not possible.”For many of you with small molecules (chemicals) and associated data (for examplestructure activity data) why not tweet your data and its related topic hashtag in ODDT?Perhaps this simple template below could be of use. Also feel free to contact us if youwant your topics added to the app so you can use ODDT to solve your molecule datasharing needs!Here is some text you could use in your grant[DATA SHARING PLANWe will share data generated during the course of this program. This will beachieved through tweeting a link to the data and use of the Open Drug DiscoveryTeams software program:(http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3503260/pdf/minf0031-0585.pdf).This software is a freely available mobile app for Apple devices and covers manyneglected and rare disease topics. Molecules and data are visible to anyone using theapp and the data is also downloadable in several formats to enable reuse. ]FAQ
  10. 10. -What platforms does ODDT run on?The user interface is provided in the form of an iOS app, which runs on iPhone, iPodand iPad devices. It can be downloaded freely from the Apple iTunes AppStore:http://itunes.apple.com/app/oddt/id517000016Versions for other platforms, such as Android and generic web, are planned, but for themoment we are focusing on the most popular app platform.-How do I interact with the ODDT app?When you download and run ODDT, you are able to browse and view any and all of thecontent, which is free and open. To interact with the system, you should ideally activateyour Twitter account. You have to configure Twitter from within the iOS system, andthen when the app requests permission to have access, you need to say yes. Once thisis done, you can endorse, disapprove or comment on factoids from within the app. Thisis done by emitting a tweet from your account. The app will never use your Twitteraccount without making it abundantly clear what is about to happen, i.e. you need topress a button labeled Tweet. Once you have connected to Twitter, you will also beable to view the statistics that are associated with your account. If you do not have aTwitter account, or do not wish to use it, you can vote on content anonymously, but yourcontributions will have less gravity, and you will not have any acknowledgment of yourparticipation.-When I tell my rare disease friends and associates about the app, can I suggest thatthey offer to add their rare disease?Later versions of the app will add more disease topics, but by all means get them tosend us the disease names to add, along with a suggested Twitter hashtag, and animage to display on the main screen.-What does the Epsilon icon on the main screen stand for?This can be used for tracking your activity, based on your Twitter account, both overalland broken down by topic. Each time you endorse or disapprove a factoid, your countgoes up. If you tweet out a link to new content, using one of the topic hashtags, and itgets endorsed by you or something else, it counts as an "injection". A "retirement" is afactoid that got deleted due to lack of endorsement, following the one week graceperiod.-Where do the topics come from?The initial choice of diseases/research topics was based on our diverse interests. Infuture app versions we plan on crowd sourcing the topics, as well as the content andranking.
  11. 11. -When I tweet something on my account that relates to topicX should I always tag itwith: #ODDT #topicXWhen you emit a tweet that has a link and one of the topic hashtags, it is assimilated asa document (internally described as a "factoid"). By default it starts with an endorsementrating of 0, which means that it will eventually be retired, unless someone endorses it. Ifyou also add the #oddt hash tag, it will auto-endorse, which means that it starts out asa factoid with a +1 ranking, and the endorsement corresponds to the Twitter accountyou used to post it.For example:1. @researcher: Progress on a cure for #malaria http://malaria.org/cure.html2. @researcher: Progress on a cure for #malaria http://malaria.org/cure.html#oddtThe first tweet starts with an endorsement of 0, and will eventually be deleted unlesssomebody endorses it. The second tweet is equivalent to the first tweet followed by@researcher endorsing it.-Are hashtags case-sensitive?No. #greenchemistry, #GreenChemistry and #GREENCHEMISTRY are all the same,but #Green_Chemistry is different.-How do I get my rare/neglected community involved ?To get your team involved just get them all tweeting the hashtag for the topic of interest.Get the scientists to share links to papers or ideas they want to put out there openly. Ifwe can create a community then we can store the information for mining later and reuseacross diseases, e.g. anyone can tweet molecules, structure activity data, summaries ofpapers, links to news etc.Encourage them to download the app, too, but they dont need an iPhone/iPad toparticipate.-Whats the difference between Incoming, Recent and Content?Incoming: all tweets that have been converted into factoids, sorted by latest first.Suitable for browsing for new content worthy of endorsing.Recent: factoids that currently have a positive ranking, i.e. there is at least oneendorsement, and the endorsements are not outweighed by disapprovals. Sorted bytime most recently updated.Content: currently similar to Recent, except that highest ranking is shown first.
  12. 12. -What sort of documents should I endorse?The ODDT project is about collating open data for research. Documents that have linksto content that resides behind paywalls should probably not be endorsed unless there isa reasonably detailed abstract or synoposis, or if the purpose is to associate links withhelpful metadata, e.g. chemical structures, or useful comments. For the disease-relatedtopics, endorsed documents should have direct or indirect relevance toward finding acure, such as the ongoing search for a drug, vaccine, antibody, gene-therapy, etc.-How is the Open Drug Discovery Teams project funded?Currently it isnt, other than limited sponsorship. The beta version was designed andbuilt by Sean Ekins and Alex M. Clark. The server is being temporarily hosted onmolsync.com. We are interested in exploring a variety of different funding opportunities.References, posters and slides on ODDTEkins S, Clark AM and Williams AJ, Open Drug Discovery Teams: A Chemistry MobileApp for Collaboration, Mol Informatics, 31: 585-597, 2012.http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3503260/pdf/minf0031-0585.pdfClark AM, Williams AJ and Ekins S, Cheminformatics workflows using mobile apps,Chem-Bio Informatics Journal, 13: 1-18 2013.https://www.jstage.jst.go.jp/article/cbij/13/0/13_1/_pdfEkins S, Clark AM and Williams AJ, Incorporating Green Chemistry Concepts intoMobile Applications and their potential uses, ACS Sustain Chem Eng, 1. 8-13, 2013.http://pubs.acs.org/doi/pdf/10.1021/sc3000509Ekins S, Waller CL, Bradley MP, Clark AM and Williams AJ, Four disruptive strategiesfor removing drug discovery bottlenecks, Drug Discovery Today, 18: 265-271, 2013.http://www.molmatinf.com/oddt.htmlhttp://www.scimobileapps.com/index.php?title=Open_Drug_Discovery_Teams
  13. 13. http://www.slideshare.net/ekinssean/oddt-open-drug-discovery-teams-for-collaborationhttp://figshare.com/articles/search?q=open+drug+discovery+teams&quick=1&x=0&y=0Please contact us for further details at: aclark@molmatinf.com andekinssean@yahoo.com. You can learn more about the ODDT app at:http://www.scimobileapps.com/index.php?title=Open_Drug_Discovery_TeamsAnd frequent blogs at http://www.collabchem.com and http://cheminf20.org.AcknowledgmentsWe thank the Royal Society of Chemistry (RSC) for sponsoring the app. Weacknowledge all those who have provided ideas for topics or whose feedback has beenincorporated into the app. Photo for tattoo for Jonah’s Just Begun (SanfilippoSyndrome) courtesy of Jill Wood www.jonahsjustbegun.org

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