Interoperable Annotation User Stories/Use Cases (Responses)
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TimestampName AffiliationI am a...User story 1Biggest challengeI am a...User story 2I am a...User story 3Biggest challenge 2Biggest challenge 3
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4/2/2016 15:30:38Maryann MartoneUCSDResearcherI am reading a scientific article in Pub Med Central and annotating it; my colleague is reading the same article at the publisher's website and annotating it. I get a notification that there are others annotating the same article and I have a means to view them where I am, with the client I am using.Document equivalence
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4/2/2016 15:35:56AnonymousBarton CollegeSTEM College Professor to be able to seed annotations for my students to view across articles from multiple sources.Paywalls
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4/3/2016 18:05:11Nicole NogoyGigaScienceEditorAs an Editor keen for more reproducible research, I would like to see all annotations on all research objects we publish (paper, data, code, workflows etc.) accross all our platforms (GigaScience, GigaDB, Giga Galaxy) and external platforms we use (protocols.io, Publons) on each version of a manuscript, including if a paper was uploaded to a pre-print server e.g. BioRxivConvincing the different platforms to implement Hypothes.is - 1) Publisher, 2) post-publication platform e.g. Publons for our open reviewer reports, 3) Reviewers to use hypothes.is to annotate the code they are reviewing for software papers. Also the underlying techy issues to enable annotations accross multiple platforms for a published paper to be seen.
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4/5/2016 11:48:53Simeon WarnerCornellResearcherto see all annotations on an article on any version of that article that I look at, be it a preprint, an institutional repository copy, or on a publisher website.Two challenges: 1) understanding which web resources should be linked, 2) avoiding any linking mechanism being used incorrectly (as a kind of spam for example)
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4/5/2016 12:51:24Sebastian Karcher
Qualitative Data Repository
Digital Archivist (?)As a repository, we want to treat annotations to an article by individual depositors as data. We want to be able to store them, and associated files (e.g. digital images, spreadsheets, etc.) and to be able for readers to read them together with the published article.The connection between repository, data, and published article.
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4/5/2016 13:08:08Rob SandersonStanford/ Gettyinformation architectAs a researcher, I want to be able to make comments on content regardless of file format and share those comments either publicly or with a group.Cross file format annotations ; group management across authentication systemsAs a cultural heritage curator, I want to tag and describe images of the objects in my collections, including the transcription of words in those images.As a web citizen, I want to discover content that has been enriched by annotations, making use of the content of the annotation as well as the annotated resource, and preferring annotations from people I know or have a high reputation in my communities.
Distinction between curator and original author
Search ; reputation models
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4/6/2016 14:36:34William GunnMendeleyscholarly communications stuff-doerAs a researcher, I want to create shareable annotations on a research paper, so that I can easily point out and discuss specific parts of a paper privately with a group of people or publicly.groups that span publishers/platforms/tool makersAs a publisher, I would like to provide easy-to-use tools to editors and reviewers so that they return more insightful, clear, and useful reviews to authors more quickly.As a toolmaker, I want to offer an interoperable annotation feature so that my users don't feel locked in and so that my tools can access a broader pool of annotations than just the ones created on my platform.
single sign-on for reviewers, editors, and authors
getting the developers to switch from the in-house solution which has already been built and works to a new system built according to specs which are still new and subject to change
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4/8/2016 14:41:29Tzviya SiegmanWileypublisherAs a publisher, I want authenticated, blinded reviewers to review articles using annotations. I want to pass reviews on along with the article even if I reject the article.blinding process
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4/11/2016 7:40:29Mark PattersoneLifePublisherAs a researcher, I want to annotate articles that are interesting to me and come back to those annotated articles all in one place.
For most people right now, the easiest way to do that is to print out the pdf, annotate it, and store it in a filing cabinet.
As a researcher, I want to be able to query an author of an article about a method, reagent or finding and have the option to share the Q&A with anyone who might be interested.As a researcher, I want to share my views on any important new paper or research output with a small group of collaborators, regardless of where it’s published/available.
Email’s probably the easiest way to do that now.
Different publishers tend to have different sets of tools.
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4/11/2016 7:41:55Mark PattersoneLifePublisherAs a researcher, I’d like to share any valuable insights into a piece of published work and gain some credit for that.
Post-publication peer review is not recognised or incentivised at the moment.
As a researcher, I’d like an easy way to get some feedback on a draft of a new research paper I’ve written, from a small group of colleagues.As a researcher, I’d like any comments that are attached to my article to be moderated (by someone) before they appear.
This adds work, but our sense is that much of our author community wants this.
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4/11/2016 7:42:50Mark PattersoneLifePublisherAs a publisher, I want a single sign-on process (ideally ORCID) for my entire site, including for annotation and other features.As a publisher, I want the ability to display annotations/discussions about our content from multiple sources, and the control to select specific sources.
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4/11/2016 14:08:28Gregg GordonSSRN
guy running a scholarly repository to make the world a better place
As a scholarly repository, we want to create connections for non-scholars to scholarly research. SSRN has played a bit with Genius.com - connecting SSRN's OA scholarly research papers to music/news.

I’d like to see the use of annotation expanded across SSRN (and other scholarly repositories) to broaden the audience, share the knowledge with more communities, and help non-scholars read/learn/apply the hard work of researchers to important decisions in their lives.
Teaching old dogs new tricks - many of the most influential scholars view annotation as cute but not scholarly
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4/12/2016 5:04:42Scott EdmundsGigaSciencePublisher (of data and narrative).As a data publisher we curate and link in as many sources of data as we can to our articles, and try to capture as much methodological detail as required, but the are always things we, the authors and reviewers fail to catch. Having a simple and recognised forum and method for readers and users to capture additional post-publication details and experience re-using our published outputs would be incredibly useful.
Requires effort. People are not used to doing this. Lack of incentives/credit if they do.
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4/13/2016 15:42:46Brooks HansonAGUPublications DirectorAs a Publisher and reader, i'd like some ability to validate users and prioritize and/or filter annotations for relevance.Limiting/filtering clutter
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4/13/2016 15:59:12Monica McCormick
NYU Libraries / NYU Press
digital publishing managerAs the publisher of a series of open access monographs in a particular subject area, I want to enable readers to add annotations, and have the authors respond to them, on a not-yet-final draft of the work. Then, I want to share selected comments from that not-yet-final draft in the final publication, to show how the author responded to earlier suggestions.
Efficiently reproducing comments from one context/publication/interface in another.
As a scholar interested in specific aspects of an online scholarly work, I want to alert my social media followers to annotations I (or others) have made on that work’s web site. I want to bring readers from the social media site back to the specific spot(s) in the text that I have annotated.
Moving the conversation back and forth between systems (e.g., Twitter and the online reading interface). Our authors want to keep the conversation on the text, or at least pointing back to the text.
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4/14/2016 10:44:09John Inglis
bioRxiv, Cold Spring Harbor Laboratory
Founder of bioRxiv, the preprint service for life scientists
As a founder of bioRxiv, the preprint service for life science, I would like to enhance the frequency and depth of commentary on manuscripts posted to bioRxiv so that feedback to preprint authors is enriched.
Single sign on. our current commenting system is Disqus.
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4/14/2016 19:42:56David MillmanNYUAs the instructor of a graduate symposium concerning a particular set of texts, I want to invite the commentary of the invited participants as annotations to those texts. I want this invited commentary visible only to the invited participants.Controlled community of participants.As the instructor of two class sections on this same set of texts, I want to allow my students in each section to see the original symposium commentary and, separately for each section, to add new annotations to the original commentary. At the end of these classes, I want my students’ commentary to be removed (perhaps transferred to another student portfolio or more generic commentary location).
Controlled community of participants plus hierarchy of annotations.
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4/15/2016 9:46:21Philip RobertsCABIAcademic content provider and UserAs a user of academic content I want to pull back search results and annotate both the search results and also each of the articles/abstracts in that search, and then export my annotations in a compatible format to work with the packages that I work within
annotating within multiple views on same data / export formats
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4/15/2016 14:31:22Tara RobenaltPLOSAs a publisher, I want all public (individual and group) annotations about our articles that happen in other tools (e.g. researcher tools) to be available (via API) so I can display them with the article for the benefit of other scientists. Conversations that benefit scientists are happening about research articles throughout a researcher's workflow; the publication site is one small step on that workflow. Annotations are one type of conversation about research and if they can be captured and linked to the source article, more will benefit.
Technologies that offer annotations on scholarly articles would need to associate the annotations to the article DOI and make the annotations available via API or deposit to an organization like CrossRef (who would have to accept such deposits). Not sure the motivation is there for a technology company to do that. The PDF is the portable form of the article, so annotations of PDFs would need to be captured and associated with the DOI. Research management tools capture article metadata, but not all annotation tools do.

Another challenge is how to minimize noise, and how to capture an entire conversation (comments/replies on an annotation).
As a peer reviewer, I would like to annotate a manuscript so I can more easily target my comments to specific sentences in the manuscript.
As a reader of scholarly articles, I would like public annotations to be linked to ORCID profiles (if they are not anonymous), so I can learn more about the annotator, and also find other annotations contributed by that person.
Versioning - as articles go through a peer review process, the manuscript is updated, and annotations may be relevant to only an early version of the manuscript. This makes it challenging to display all reviewer comments in a meaningful way.
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4/15/2016 14:34:18Tara RobenaltPLOSAs a technologist, I want standard tagging for annotations so future technologies being developed can scrape a site and identify annotations. If an annotation is public, tagging it appropriately will make it portable to other technologies.
Standardizing the tagging and getting all technologies to apply them appropriately. Providing context for an annotation picked up from a site may be difficult.
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