Open web-based annotation: Creating a lightweight, portable knowledge layer over biomedicine

Transcription

1 Open web-based annotation: Creating a lightweight, portable knowledge layer over biomedicine Maryann E. Martone, Director of Biosciences BioCADDIE webinar, Thurs Dec 10, 2015

2 Our Mission Build, deploy and nurture an open, interoperable annotation layer over the Web, enabling a conversation over all knowledge. Nature: Annotating-the-scholarly-web

3 The problem Right now, you can only have a conversation on a very small part of the web. the web Where comments exist they re: below the fold, page-level comments only proprietary & closed low tech poorly moderated controlled by the site owner different account for every site the web w/ comments

4 The problem the web On the rest of the Web, you can only have a conversation at a distance from the source material, on platforms like Reddit, Twitter, HackerNews, Facebook and .

5 An alternative exists: Web Annotation Works as a layer over any web page or PDF *(images, video and data coming) Open source Standards based Mission driven Easy-to-use

6 Web Annotations should be just like the Web Based on an emerging W3C standard. Any compatible client can create them. Any compatible server can deliver them. A client can listen to whichever sources of annotations the user wants to, including multiple sources simultaneously. No one controls them. No one has a monopoly over the format. The software and the service providers are not locked together.

7 Hypothes.is in action: demo

8 Demonstration: Basic Functions Installing Hypothes.is Annotating with Hypothes.is Viewing annotations Public-private-groups Tagging Replying Links-inserting images Searching the stream

9 Annotation in science and biomedicine

10 Biomedical scientists annotate Annotation is ubiquitous across biomedicine, although of different types: Marginalia: Personal notes or thoughts on part of a document or piece of data Communication: Comments, clarifications questions about an object or part of an object Knowledge extraction: Curators from databases or dedicated student curators for an individual project, create structured annotations by extracting information from research objects Knowledge addition: Adding human knowledge to parts of data, e.g., gene sequences, images, linking information, citation

11 Science is done by teams and in stages: many tools, many people, many places Analyze 3D vesicle Experiment Fixation didn t go well Vesicle is enlarged Electron micrograph of neuron Lot s of precipitates What antibody did they use? We didn t think it necessary... Golgi is not affected Why didn t you perform a smoothing step? I ve decided to accept this paper, but please revise... Write and revise I didn t find that to be true I heard that mouse was not a complete knockout Agrees with... Publish Knowledge is added incrementally at every step but rarely transfers Post-publication review ; Literature curation I should renalyze my data

12 Current uses Peer review Post publication review Journal club In the classroom Updating content Structured annotation Making content more accessible Automated annotations

13 Post-publication peer review Quick and universal way to provide feedback on published articles

14 Climate Feedback A group of approximately 80 high profile climate scientists use Hypothesis to annotate climate news and reporting that have directly led to corrections and updates to articles as a result. With our new groups capability, they will be expanding coverage this next year. Read: Guardian story on them

15 Living documents: Updates Neuroscientist annotating her own paper to provide updates and additional information

16 Making science accessible Science in the Classroom: AAAS has grad students annotating Science Magazine for teaching purposes using Hypothesis

17 Opening up communication channels around scientific articles

18 Hypothes.is in the classroom Educators are using annotation to enable students to learn dynamically and socratically both in remote classrooms and as a part of a flipped or blended classroom experience. Graduate students at New Mexico State annotating scholarly journal articles (note PDF annotation

19 Using Hypothes.is for structured annotation David Kennedy, NITRC General purpose, web-enabled tool for curation of the literature

20 Resource Iden,fica,on Ini,a,ve: New type of resource cita,on Have authors supply appropriate iden2fiers for key resources used within a study such that they are: Machine processable (i.e., unique iden2fier that resolves to a single resource) Outside of the paywall Uniform across journals and publishers Pilot project An2bodies SoHware/databases Gene2cally modified animals hkps://

21 An independent communication channel across the literature: Machine generated annotations 1. Script recognizes Research Resource Identifiers in published papers 2. Highlights RRID s in web page 3. Imports information from NIF database Machine-generated annotations piped through Hypothes.is

22 A reproducibility layer over science What if over any paper we could know: Has the paper been retracted? Which antibodies and reagents does it use? Have any issues been reported with them? Who else has tried to reproduce this protocol? Are there any additional notes by the authors since original publication? What do my peers think of this? Does anyone have helpful suggestions? These things are possible now, and we are putting the partnerships together to enable them.

23 Bringing open annotation to all research objects " Data annotation is a major use case in biomedicine Hypothes.is provides an ideal tool for metadata curation and exploring data repositories Pilot project: Integration of Hypothes.is into all data repositories

24 Hypothesis: Curation tool for data repositories Curators extract key values from the published literature Hypothesis was used to create a rapid prototype of a curation tool, capable of supporting crowdsourcing Created by graduate student Vanessa Sochat in < 1 day NeuroVault.org

25 Data With Hypothesis you can annotate any cell of any.csv file on the web, collaboratively with anyone else-- even though you don t control the file. We re now exploring how to do that for other forms of data, images and video.

26 In production Gigascience just added annotation to to GigaDB abstract pages. Annotating the actual data sets will follow.

27 What s next?

28 Who is annotating? Allow authors to tie annotations to their ORCIDs (unique author identifiers) Goals: Give authors scholarly credit for annotations* Provide readers with a means to evaluate the expertise of the annotator Surface role-based annotations, e.g., author, editor * Timeline: First integration, Q Also working with Altmetrics

29 Many formats Hypothesis works on HTML and PDF now, along with some forms of tabular data. EPUBs will follow shortly. Images will happen next year, video will follow. We ll also start working on integrations into popular apps such as PDF readers and bookreaders.

30 Support for structured annotations Tag with controlled vocabularies Export in structured format Better search Annotation dashboard

31 Annotating All Knowledge We are partnering with >40 leading organizations in academic publishing, platforms and libraries to bring the world s scholarship online with web annotation within 3 years. Consumer publishers will follow. JSTOR, PLOS, Europe PubMed Central, arxiv, biorxiv, Hathi Trust, Ubiquity Press, elife, SSRN, ipython / Project Jupyter, Wiley, JHU Project MUSE, Stanford University, University of Illinois, ORCID, Open Journal Systems / PKP and others. Build this new function (open annotation) into all scholarly platformsinteroperable, portable, open annotations as a core function for scholarship

32 Our Team

33 Funders

34 Selected and Recent Press

35 Global Biodiversity using our API and a crawler to provide automated annotations of latitude and longitude w/ a map layer.