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Lost In Translation
when machines meet
STM content…
This presentation was designed to be delivered live. To help you
under...
3
Questions…
Behind the shared vision held by the partners of the Resource
Identification Initiative lies a number of ques...
Which one?

REPRODUCIBILITY: In the scientific community it is difficult to find
objective qualitative information about r...
Where is it?

EFFICIENCY: Poor resource visibility means that labs around the world
waste thousands of man hours duplicati...
Who has
used it?

CONNECTIVITY: By its nature, science is a collaborative endevour.
Efficiently identifying knowledge and ...
The Role of
Content..
Research content has evovled over time as a means of communicating
conclusions. However, the real un...
Who has used it?
Where is it?
Every article contains valuable information about experimental
procedures and materials. Whe...
Challenges..
Todays research articles are designed to be read one at a time by
humans. To cross reference we rely on our n...
1 2 3
XML

Ambiguity

Culture

1) Every publisher has slightly different XML standards.
2) The vocabularly for describing ...
XML

The XML produced by different publishers can be significantly different.
This makes indexing and analysing content at...
Ambiguity

Insufficient annotation and naming in content makes it difficult to
disambiguate material entities. Take this g...
Sigma produces at least 5 variations of glass beads, which version is
being referred to in the article?
Culture

Vs
Publishers have traditionally made money by attracting great content and
selling access to as many people as p...
Who is
involved..
The RII is backed a wide group of interests working together to change
how experimental resources are do...
The group includes publishers, academic groups, funding agenicies,
resource repositories and commercial companies…
Shared Goals..
The group has a number of shared goals with the aim of improving the
machine accessiblity of STM content in...
1. Unique Identifier

AB_1234578
1) By agreeing and assigning standard unique identifiers for all known
research materials...
2. Editor Awareness

• Drive adoption
• Better XML standards
• Content machine friendly
2) By working with publishers and ...
3. Distribution…

3) By developing technology and APIs to diseminate research material
information in a standarised form…
4. Annotation

4) While NIF is focussing on research material annotation at the prepublication stage, scrazzl is working o...
5. Interoperability

5) One of the main aims of the RII is to support the adoption of a
standardised public research mater...
Our
Destination…
So what does success look like?
Connectivity

Every new article published will contain unique identifiers either in the
visible text or in the underlying ...
Reproducibility

Data driven qualitative metrics of material entities will be available,
improving reproducibility and dri...
Visibility

Improved Geo and time dependent resource availability visualisation will
be possible. Finding where resources ...
Questions?
E: david.kavanagh@scrazzl.com
T: +353 (0) 863-867-990
Twitter: @dkavanagh
www.scrazzl.com
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Lost In Translation when machines meet STM content

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This slidedeck outlines the Resource Identification Initiative and how partners within the group are working to improve reproducibility in science by making experimental methods more machine readable.

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Lost In Translation when machines meet STM content

  1. 1. Lost In Translation when machines meet STM content… This presentation was designed to be delivered live. To help you understand the content we have added these notes…
  2. 2. 3 Questions… Behind the shared vision held by the partners of the Resource Identification Initiative lies a number of questions. …
  3. 3. Which one? REPRODUCIBILITY: In the scientific community it is difficult to find objective qualitative information about research materials. Choosing the wrong products often means failed experiments…
  4. 4. Where is it? EFFICIENCY: Poor resource visibility means that labs around the world waste thousands of man hours duplicating eachothers work. Greater visibility of produced research materials would dramatically improve efficiency in science and reduce waste. ..
  5. 5. Who has used it? CONNECTIVITY: By its nature, science is a collaborative endevour. Efficiently identifying knowledge and expertise when required is key to progressing discovery. ..
  6. 6. The Role of Content.. Research content has evovled over time as a means of communicating conclusions. However, the real untapped value in content is the information about the journey…
  7. 7. Who has used it? Where is it? Every article contains valuable information about experimental procedures and materials. When cross referenced with location, author and time data, powerful new experimental and research insights are Which one? revealed…
  8. 8. Challenges.. Todays research articles are designed to be read one at a time by humans. To cross reference we rely on our notetaking, memory and prior knowledge. Machines have the potential to dramatically improve the efficiency of how we glean insight from content. But….
  9. 9. 1 2 3 XML Ambiguity Culture 1) Every publisher has slightly different XML standards. 2) The vocabularly for describing research entities is ambiguous. 3) There is a poor culture of facilitating data mining and enforcing best annotation practice in the publishing industry.
  10. 10. XML The XML produced by different publishers can be significantly different. This makes indexing and analysing content at scale challenging…
  11. 11. Ambiguity Insufficient annotation and naming in content makes it difficult to disambiguate material entities. Take this glass beads example….
  12. 12. Sigma produces at least 5 variations of glass beads, which version is being referred to in the article?
  13. 13. Culture Vs Publishers have traditionally made money by attracting great content and selling access to as many people as possible . Advances in technology have largely been viewed by publishers as a means to do more of the same at a lower cost. Publishers have been slow to adopt practices that make their content machine accessible…
  14. 14. Who is involved.. The RII is backed a wide group of interests working together to change how experimental resources are documented in new research content…
  15. 15. The group includes publishers, academic groups, funding agenicies, resource repositories and commercial companies…
  16. 16. Shared Goals.. The group has a number of shared goals with the aim of improving the machine accessiblity of STM content in a practical and sustainable way…
  17. 17. 1. Unique Identifier AB_1234578 1) By agreeing and assigning standard unique identifiers for all known research materials (commercial and non-commercial)…
  18. 18. 2. Editor Awareness • Drive adoption • Better XML standards • Content machine friendly 2) By working with publishers and other community members to encourage the inclusion of unique indentifiers at the authoring stage and devising strategies for XML standardisation...
  19. 19. 3. Distribution… 3) By developing technology and APIs to diseminate research material information in a standarised form…
  20. 20. 4. Annotation 4) While NIF is focussing on research material annotation at the prepublication stage, scrazzl is working on a seperate initiative to drive retrospective annotation of published research… - Pre-publication - Prospective - Post-Publication - Retrospective
  21. 21. 5. Interoperability 5) One of the main aims of the RII is to support the adoption of a standardised public research material onthology and vocabulary that is interoperable with other exsisting biological onthologies…
  22. 22. Our Destination… So what does success look like?
  23. 23. Connectivity Every new article published will contain unique identifiers either in the visible text or in the underlying metadata. This will improve machine readability and will dramatically improve the semantic connectivity of articles…
  24. 24. Reproducibility Data driven qualitative metrics of material entities will be available, improving reproducibility and driving efficiency..
  25. 25. Visibility Improved Geo and time dependent resource availability visualisation will be possible. Finding where resources are and identifying key technical experts will be more efficient…
  26. 26. Questions? E: david.kavanagh@scrazzl.com T: +353 (0) 863-867-990 Twitter: @dkavanagh www.scrazzl.com

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