Dk net webinar tutorial pen
- 1. Introduction to dkNET: Overview and use cases
- 2. Outline of presentation 1. Introduction to dkNET 2. Introduction to SciCrunch platform 3. Overview of structure and content of dkNET portal 4. Tutorial Searching through dkNET Signing up for an account Saving searches Signing up for search alerts Creating collections Citation/usage analytics 5. Free session
- 3. Informatics and the Data Deluge • It is quite difficult to access, collate, and filter the incredible array of information and data in the public domain. • dkNET was established in recognition of the need to interconnect research communities, both basic and clinical, by providing seamless access to large pools of resources and data relevant to the mission of NIDDK. • dkNET provides a single point-of-entry for discovering this information to allow researchers to make good decisions in the research process, thereby increasing both the speed and efficiency of the process. 3
- 4. Database Software Application Data Analysis Service Topical Portal Core Facility Ontology Software Resource Years: dkNET Offers… • A search portal to find community- vetted research resources: materials, data and tools for your research • Access to hundreds of databases across biomedicine with one easy search • Personalized search and display of results • Information hub for community news and social networking • Support for resource providers http://dknet.org @dknet_Info
- 5. dkNET Investigator's RetreatJune16, 2014 Shared Resources dkNET is built on the SciCrunch platform Resource Identification Portal Neuroscience dkNET Drug Design • Pull from and push to a common pool of data • Customize according to communities • Common interface elements across platforms
- 6. How to use dkNET
- 7. dkNET ESP mtg 06/15/16 Register for dkNET for customized functions Help and Tutorials available under About
- 8. Type 1 diabetes: One path
- 9. Simultaneous search across 3 indices Results are returned in order of specificity, i.e., Community resources are presented first if they are available. But all searches are executed across indices Community More resources Literature Specialized NIDDK-relevant resources 200+ databases across biomedicine Literature
- 10. Community resources NURSA BCBC DiaComp GUDMAP T1DB MMPC NIDDK Central Repository dkNET Community Funding AddGene: Plasmids Clinical trials.gov: Clinical trials and data Antibody Registry: 2M+ antibodies Integrated animals: Model organism databases SciCrunch Resource Registry: 13K+ tools Grants.gov NIDDK-funded resources and centers Additional relevant databases vis SciCrunch
- 11. Community resource navigation ● Organized according to main categories of research resources ● Subcategories are specific to each category ● Faceted search to drill down into a single source Search tip: Start with a general term, and use the facets and filters to refine your search
- 12. Demo: Search and Display in Community Resources Search: Rodent models for Type 1 Diabetes
- 13. Type 1 diabetes: One path 2. Select “organism” 1. Enter: Type 1 diabetes into the search bar 3. Click search icon
- 14. Results from Community resources Navigation: Click on “Any” to remove “Organism” filter Individual records in snippet view Feedback Category: Organism
- 15. Narrowing down search results • Using categories and subcategories • Category graph for overview and faceting • Snippet view vs table view • Using facets and filters within a source • Exporting results
- 16. Community view: Subcategory vs source • Use the facets in the side panel to narrow down results • Select by subcategory or source • Subcategory: results presented across all sources as snippets • Source: Results are returned from a single source as a table
- 17. 3 sources Click to view record details Click to view details about the source Alert: This resource is archival Add to a personal collection Snippet view: Each record is displayed separately
- 18. Selecting a source reveals specialized facets and filters Expand number of columns visible Source specific facet; click to view unique filters Executes filtered search Export results as CSV (1000 result limit) Table view: Displays records within a single source
- 19. Make sure to click “Perform search” after selecting filters. May have to scroll down a bit. Select filter Remove filter
- 20. Search tip: Navigation Use the breadcrumbs in the upper right corner of the search window to return to an earlier state Click organisms to go back to original search results
- 21. Explore another source: DiaComp
- 22. Structure of dkNET Rodent models of Type 1 diabetes 1. Type 1 diabetes 2. Organism 3. Mouse 4. Integrated animals 5. Phenotype 6. Mouse 7. DiaComp Data View Category SubcategoryMore Literature Materials Data Resource Protocols Organism Rat Community Fly Worm Source Facet MMPC BCBC Species Background Gene DiaComp Phenotype Integrated Mouse
- 23. Short cut Use the category graph to get an overview of categories and sources and use it to select search results Available at the top of the left side panel Selects: Integrated animals + mouse
- 24. Creating a collection When browsing in snippet view, you can create a custom collection of search results within or across sections. Collections are saved in your account and can be added to at a future date. You must have an account and be logged in to use this feature Select existing collection or create a new one. Then click on + to add item Add to or remove item from collections by clicking the + or - Click icon next to record to add to a collection Icon turns green when item is in a collection. Click to view collection
- 25. Viewing and Managing Collections
- 26. Using vocabulary services and other search tips • Putting quotes around a phrase, e.g., “Type 1 diabetes” will search for the entire phrase. With no quotes, dkNET interprets query as Type + 1 + diabetes, accounting for some false positives • dkNET will attempt to match search terms to community ontologies to provide synonyms, acronyms and related terms. Click “Query expansion” to view additional terms. Synonyms and acronyms may be removed if they cause false positives. • Terms may also be selected from the pull down menu • dkNET supports boolean operators, “AND”, “OR” and - (=NOT) • Searches may be saved (account required for saving beyond current session)
- 27. Select: Type 1 diabetes mellitus from pull down menu Note that “” are placed around the term to search for the entire phrase; synonyms etc are joined by an “OR” Autocomplete adds two useful synonyms “Type 1 diabetes mellitus” OR “IDDM” OR “insulin- dependent diabetes mellitus”
- 28. Creating a boolean query • Search terms may be joined manually by adding “AND” and “OR” ; the default is AND • Adding a - before a term executes a NOT query, e.g., excludes search results with that term Manually added “Type 1 diabetes” and “juvenile diabetes” joined by OR “Type 1 diabetes mellitus” OR “IDDM” OR “insulin-dependent diabetes mellitus” OR “Type 1 diabetes” OR “juvenile diabetes” Manually added terms are joined with vocabulary expansions
- 29. Saving searches Search strings can be saved for future use • You must have an account and be logged in to save searches for future sessions • You can sign up for alerts to be notified when new or updated records are added to dkNET Click here to save a new search Click here to set up notification preferences Run a previously saved search Click to save search or run a previously saved search Note that saved search will save not only the the search terms but also selected categories, filters and facets
- 30. Demo: Using More Resources and Literature Find: Cell lines for Type 1 Diabetes
- 33. Navigation in More Resources • Snippets are individual sources • Categories are different system levels or data types More resources index Over 200 sources are available from across biomedicine Click to view categories
- 34. Each index is organized slightly differently Community More resources Literature Navigation differs across indices Resource categories Sources Data and/or resource type System level Individual records Source Functions and filters Results display Functions and filters Results display Collections and Analytics Analytics Facets Articles Functions and filters Results display
- 35. Several sources have information • Selecting “Cell” from system level or “Cell lines” from Type of data will return a list of sources with results • Selecting a source will pull up custom filters • Note: Collections are not available from the More Resource menu
- 36. Featured resource: Cellosaurus-integrated cell line directory New resources are constantly being added via other SciCrunch communities
- 37. dkNET Literature Synonyms Easy to browse abstracts Easy sorting functions Altmetrics
- 38. Review: Simultaneous search across 3 indices Results are returned in order of specificity, i.e., Community resources are presented first if they are available. But all searches are executed across indices Community More resources Literature Specialized NIDDK-relevant resources 200+ databases across biomedicine Literature
- 39. dkNET connects resources Social media Research resource analytics Other SciCrunch communities More resources LiteratureCommunity RRID’s
- 40. RRIDs An easy, practical method for improving reproducibility and transparency
- 41. dkNET ESP mtg 06/15/16 Unique ID’s for all! Resource Identification Initiative • It is currently impossible to query the biomedical literature to find out what research resources have been used to produce the results of a study • authors don’t provide enough information to unambiguously identify key research resources • Impossible to find all studies that used a resource • Critical for reproducibility and data mining • Critical for trouble-shooting Faulty Antibodies Continue to Enter US and European Markets, Warns Top Clinical Chemistry Researcher-Genome Web Daily, October 11, 2013
- 42. dkNET ESP mtg 06/15/16 Authors supply database accession numbers for key research resources used in research
- 43. Resource IDs from NIF aggregated databases •A single portal for authors •>25 authoritative databases •One search interface •Simple directions •Prominent “Cite This” button •Help desk RII Portal http://scicrunch.org/resources
- 44. Which Journals now ask for RRIDs? • ~25 Elsevier Journals – • BMC – • Frontiers • Cell Press • Wiley (JCN, J. Neuro. Research, Brain and Behavior) • Endocrine Soc journals? http://scicrunch.com/resolver/RRID:nlx_144509 Nagging authors is most effective, typesetting allows apps to run smoothly
- 45. Who is using…tracking resource usage • dkNET provides tools and services for identifying and tracking research resources • Resource providers: who is using my resource? • Individual researchers: Who is using this resource and what other resources are related to it?
- 46. What is a good antibody against CART? Query: CART Materials > Antibodies > Antibody Registry (81 results)
- 47. Click on category to sort
- 49. Who is using my resource? For resource providers… Query: My resource Category: Resources
- 50. dkNET ESP mtg 06/15/16 Type in Your Resource and Search
- 51. dkNET ESP mtg 06/15/16 Select your resource Click on resource name
- 52. dkNET ESP mtg 06/15/16 Subscribe to New References and/or Claim Ownership Lists mentions in the open access literature
- 53. dkNET ESP mtg 06/16/16 Resource Analytics
- 54. dkNET ESP mtg 06/15/16 Manage Resource References Subscription
- 55. dkNET ESP mtg 06/15/16 Manage Resource Reference Subscription: Choose to subscribe or unsubscribe to user notifications via the dkNET website and/or e-mail
- 56. Some use cases to try Q1. Funding Opportunities Find funding opportunity announcements related to obesity that expire in 2016. Q2. Research Materials Can you find validated monoclonal antibodies against Thyroid Stimulating Hormone Receptor (TSHR) or thyrotropin receptor? Q3. Clinical Trials How many clinical trial datasets related to type 1 diabetes are available? Q4. Model Organisms Can you find animal models of polycystic kidney disease? Q5. I’m looking for animal models for Type 1 diabetes DiaComp has 3 mice listed and Rat Genome Database has 1 rat strain listed that are asserted to be models of Type 1 diabetes (and 2 more that might be relevant). Can you find them?