Annotopia open annotation services platform

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Annotopia is an open-access, open-source, open annotation services platform developed for scientific annotation of documents and datasets on the web using the W3C Open Annotation model http://www.openannotation.org/spec/core/. Using Annotopia, virtually any client application including lightweight web clients, can create, selectively share, and access annotation of web documents and data. This can be done regardless of the ownership of the base objects being annotated. Annotopia supports unstructured, semi-structured and fully-structured (semantic) annotation; manual and automated (textmining) annotation; permissions, groups, and sharing. It also provides access to specialized vocabulary and text analytics services. Annotopia is an open source platform licensed under Apache 2.0.

Science

the Annotopia
Open Annotation Services
Platform
25 February 2014
Paolo Ciccarese & Tim Clark
Massachusetts General Hospital
Harvard Medical School
© 2014 Massachusetts General Hospital

Canonical information
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Canonical information
Canonical information Laboratory data

Canonical information
Canonical information Laboratory data
Linear narrative
Canonical informationCanonical informationCanonical information

RDF
Bob: They used PDAPP mice to show this.
Alice: Not sure model is good - seizures.
Bob: Reproduce on another model.

Annotopia
• Annotopia is an open source, multimedia annotation
repository.
• It holds structured and unstructured annotation in
a formal standardized model…
• Using the W3C Open Annotation model (W3C
OA), serialized as JSON-LD.

Goals
• Web & PDF annotation
• comments, semantic tags, claim-evidence
• private, group, & institution permissions
• image-specific annotation
• Bibliographic entity resolution

Open APIs
• Client side
• Utopia, Domeo, annotator.js, …
• Services side
• Standard textmining connectors
• Vocabulary services
• Mashup injection

+
Literature Services
+
+
Textmining
Services
…

Early installations
• Harvard/MassGeneral ✔
• Eli Lilly Research Labs, UK ✔
• University of Manchester ✔
• European Bioinformatics Institute (planned)

Annotate in Utopia or Domeo
visible in both

Call textmining services
& approve relevant tags

Some Current Collaborators
• Harvard Medical School / MGH (Tim Clark, Paolo Ciccarese)
• Eli Lilly Research UK (Derek Marren, Director Bio IT)
• Elsevier (Brad Allen, Chief Architect)
• OpenPHACTS (Lee Harland, Paul Groth)
• EMBL / EBI / Europe PubMed Central (Jo McEntyre)
• Force11 Resource Identification Initiative (Maryann Martone)
• Harvard IQSS / Dataverse (Merce Crosas, Gary King)

Annotopia Version
Deployment
• Version 0: Domeo web repository.
• Version 1: EOQ1 2014. Domeo + Utopia basic
annotation services.
• Version 2: EOQ2 2014. Annotator.js API. Semantic
tagging, micropublications, textmining integration.
• Version 3: EOQ3 2014. Mashup services.
FAIRPORT integration.

Technical Workshop
European Bioinformatics Institute
April 29, 2014
contact: Jo McEntyre, mcentyre@ebi.ac.uk
pharma participants invited

• Science-based Open Annotation services
• Metadata storage and discovery for documents,
data, and other resources
• Integrate textmining and vocabulary services
• Web annotation & metadata as first-class objects
• Open source under Apache 2.0 license

Annotopia open annotation services platform

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We characterize the earliest galaxy population in the JADES Origins Field (JOF), the deepest imaging field observed with JWST. We make use of the ancillary Hubble optical images (5 filters spanning 0.4−0.9µm) and novel JWST images with 14 filters spanning 0.8−5µm, including 7 mediumband filters, and reaching total exposure times of up to 46 hours per filter. We combine all our data at > 2.3µm to construct an ultradeep image, reaching as deep as ≈ 31.4 AB mag in the stack and 30.3-31.0 AB mag (5σ, r = 0.1” circular aperture) in individual filters. We measure photometric redshifts and use robust selection criteria to identify a sample of eight galaxy candidates at redshifts z = 11.5 − 15. These objects show compact half-light radii of R1/2 ∼ 50 − 200pc, stellar masses of M⋆ ∼ 107−108M⊙, and star-formation rates of SFR ∼ 0.1−1 M⊙ yr−1 . Our search finds no candidates at 15 < z < 20, placing upper limits at these redshifts. We develop a forward modeling approach to infer the properties of the evolving luminosity function without binning in redshift or luminosity that marginalizes over the photometric redshift uncertainty of our candidate galaxies and incorporates the impact of non-detections. We find a z = 12 luminosity function in good agreement with prior results, and that the luminosity function normalization and UV luminosity density decline by a factor of ∼ 2.5 from z = 12 to z = 14. We discuss the possible implications of our results in the context of theoretical models for evolution of the dark matter halo mass function.

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Annotopia open annotation services platform

3. Canonical information Canonical information

4. Canonical information Canonical information Laboratory data

5. Canonical information Canonical information Laboratory data Linear narrative Canonical informationCanonical informationCanonical information

6. RDF Bob: They used PDAPP mice to show this. Alice: Not sure model is good - seizures. Bob: Reproduce on another model.

7. RDF Bob: They used PDAPP mice to show this. Alice: Not sure model is good - seizures. Bob: Reproduce on another model.

8. Annotopia • Annotopia is an open source, multimedia annotation repository. • It holds structured and unstructured annotation in a formal standardized model… • Using the W3C Open Annotation model (W3C OA), serialized as JSON-LD.

9. + =

10. Goals • Web & PDF annotation • comments, semantic tags, claim-evidence • private, group, & institution permissions • image-specific annotation • Bibliographic entity resolution

11. Open APIs • Client side • Utopia, Domeo, annotator.js, … • Services side • Standard textmining connectors • Vocabulary services • Mashup injection

12. + Literature Services + + Textmining Services …

13. Early installations • Harvard/MassGeneral ✔ • Eli Lilly Research Labs, UK ✔ • University of Manchester ✔ • European Bioinformatics Institute (planned)

14. Load and preprocess document

15. All references become objects

16. Make comments localized on text

17. Annotate in Utopia or Domeo visible in both

18. Annotate images

19. Annotate images

20. Call textmining services & approve relevant tags

21. Create micropublications

22. Annotate & share micropublications

23.

24. Some Current Collaborators • Harvard Medical School / MGH (Tim Clark, Paolo Ciccarese) • Eli Lilly Research UK (Derek Marren, Director Bio IT) • Elsevier (Brad Allen, Chief Architect) • OpenPHACTS (Lee Harland, Paul Groth) • EMBL / EBI / Europe PubMed Central (Jo McEntyre) • Force11 Resource Identification Initiative (Maryann Martone) • Harvard IQSS / Dataverse (Merce Crosas, Gary King)

25. Annotopia Version Deployment • Version 0: Domeo web repository. • Version 1: EOQ1 2014. Domeo + Utopia basic annotation services. • Version 2: EOQ2 2014. Annotator.js API. Semantic tagging, micropublications, textmining integration. • Version 3: EOQ3 2014. Mashup services. FAIRPORT integration.

26. Technical Workshop European Bioinformatics Institute April 29, 2014 contact: Jo McEntyre, mcentyre@ebi.ac.uk pharma participants invited

27. • Science-based Open Annotation services • Metadata storage and discovery for documents, data, and other resources • Integrate textmining and vocabulary services • Web annotation & metadata as first-class objects • Open source under Apache 2.0 license

Annotopia open annotation services platform

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