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  2. Open Data – 2 | petermr's blog

    https://blogs.ch.cam.ac.uk/pmr/2007/11/19/open-data-2/
    17 Jan 2022: But the data world needs a generic term for the same reason that the publication world does. ... In all these it’s commonplace to download the whole data – for example we state “Each MACiE entry in the database can be downloaded separately as a CML
  3. Capturing SPECTRa | petermr's blog

    https://blogs.ch.cam.ac.uk/pmr/2007/12/09/capturing-spectra/
    17 Jan 2022: In any case people can download the data and reuse if it is labeled Open Data on submission (our definition). ... Because tools are Open Source it doesn’t follow that the data are.
  4. Leo Waaijers: DARE to Inspire | petermr's blog

    https://blogs.ch.cam.ac.uk/pmr/2008/03/14/leo-waaijers-dare-to-inspire/
    17 Jan 2022: I could download one and within a minute[] OSCAR had read much of the chemical data from it. ... It changes the way we should capture and publish data. The Netherlands can justly feel proud in leading the world with the coherence and commitment of their
  5. CrystalEye and repositories: distribution and integrity (cont) |…

    https://blogs.ch.cam.ac.uk/pmr/2007/11/05/crystaleye-and-repositories-distribution-and-integrity-cont/
    17 Jan 2022: PMR: see intro] […]. However, I would suggest that the experience with GenBank and other bioinformatics data sets, as well as PubChem, has been that some sort of bulk download is useful. ... The data corpus of CrystalEye, that’s what I would like to
  6. What is strongOA? | petermr's blog

    https://blogs.ch.cam.ac.uk/pmr/2008/04/30/what-is-strongoa/
    17 Jan 2022: OA means that any user, anywhere, who has access to the Internet, may link, read, download, store, print-off, use, and data-mine the digital content of that article [PMR: without ... These include the BBB declarations [above] and the The Open Knowledge
  7. https://blogs.ch.cam.ac.uk/pmr/2007/09/24/cdks-diazonamide-and-general…

    https://blogs.ch.cam.ac.uk/pmr/2007/09/24/cdks-diazonamide-and-general-thoughts-on-openness/feed/index.xml
    17 Jan 2022: The deposition process is under beta-testing and anyone can download the data (we will give away the entire structure collection shortly). ... The deposition process is under beta-testing and anyone can download the data (we will give away the entire
  8. Depositor's checklist | Research Data Management

    https://www.data.cam.ac.uk/depositors-checklist
    9 Nov 2022: you may still wish to have a Readme file that users can download together with your data files. ... OneDrive, Dropbox, Google Drive) to your data so that we can download the files.
  9. experiment and theory – the liberation of data and source |…

    https://blogs.ch.cam.ac.uk/pmr/2007/05/03/experiment-and-theory/
    17 Jan 2022: These are truly excellent statistics if you consider that this is an open access system where people are depositing data, that these data are free to download and utilize even for ... The data in the literature can be awful – some measurements differ
  10. Open Data Means Better Science | petermr's blog

    https://blogs.ch.cam.ac.uk/pmr/2011/07/02/open-data-means-better-science/
    17 Jan 2022: Cambridge. What’s Open Data? By open data we mean that it is freely available on the public internet permitting any user to download, copy, analyse, re-process, pass them to ... Open data button is a easier way to access the data with no tension of
  11. petermr's blog | A Scientist and the Web | Page 126

    https://blogs.ch.cam.ac.uk/pmr/page/126/
    17 Jan 2022: When we did try scraping the data our best estimate was about 90,000. ... So, in  principle, anyone could download our data and prove us wrong (or hopefully, concur with our findings), and we hope that our  repositories (SetupX and BinBase) will become
  12. Dissemination of CrystalEye | petermr's blog

    https://blogs.ch.cam.ac.uk/pmr/2007/10/31/dissemination-of-crystaleye/
    17 Jan 2022: These are almost completely orthogonal. Copying the data and redisseminating without reference to the originators it is, in effect, forking (see below). ... I wish you luck resolving this so that we can access the data.
  13. CrystalEye: request for subsets | petermr's blog

    https://blogs.ch.cam.ac.uk/pmr/2007/11/05/crystaleye-request-for-subsets/
    17 Jan 2022: The data corpus of CrystalEye, that’s what I would like to download. ... But my interest would not be in setting up CrystalEye2, but would be to have access to the data to:. –
  14. ACS Open Choice allows full re-use | petermr's blog

    https://blogs.ch.cam.ac.uk/pmr/2009/03/25/acs-open-choice-allows-full-re-use/
    17 Jan 2022: ACS Open Choice articles are fully open access in the sense that the licence [PDF link] allows users – for non-commercial research and education purposes – to “access, download, copy, display and ... redistribute articles as well as adapt,
  15. Does “Open API” mean anything? | petermr's blog

    https://blogs.ch.cam.ac.uk/pmr/2010/08/29/does-open-api-mean-anything/
    17 Jan 2022: There is no algorithm to expose the whole data. By contrast you can, in principle, download the whole of an Open system. ... Pingback: Mendeley and Openness |. Pingback: Dear publisher, is the data open? « Research Remix.
  16. Open Notebook NMR – motivations and confusions | petermr's blog

    https://blogs.ch.cam.ac.uk/pmr/2007/10/24/open-notebook-nmr-motivations-and-confusions/
    17 Jan 2022: If you cannot download the data and remove bad data points etc and return the data to Christoph/NMRShiftDB with commentary then I remain confused about the rights around Open Data. ... If you cannot download the data and remove bad data points etc and
  17. CrystalEye and repositories: Jim explains the why and how of Atom |…

    https://blogs.ch.cam.ac.uk/pmr/2007/11/05/crystaleye-and-repositories-jim-explains-tthe-why-and-how-of-atom/
    17 Jan 2022: have time right now): –. AD: However, I would suggest that the experience with GenBank and other bioinformatics data sets, as well as PubChem, has been that some sort of bulk download ... Andrew Dalke)… and earlier …. … using a system like
  18. Chemspider and "Open Chemistry Web" | petermr's blog

    https://blogs.ch.cam.ac.uk/pmr/2007/10/13/chemspider-and-open-chemistry-web/
    17 Jan 2022: The freedom is for an unspecified timescale and you cannot download significant amounts of the data and you cannot re-use it without permission. ... Note that even if you upload data and metadata you are not allowed to download it (there is a limit of
  19. Mendeley API Binary Battle: IsItOpenData? | petermr's blog

    https://blogs.ch.cam.ac.uk/pmr/2011/03/10/mendeley-api-binary-battle-isitopendata/
    17 Jan 2022: The presence of John Wilbanks on the team. My acid test is” Can I systematically download all of the data in the Mendeley data base, transform it to my own format, ... Hi Peter,. All very good and valid questions raised there. To answer you acid test:
  20. petermr's blog | A Scientist and the Web | Page 59

    https://blogs.ch.cam.ac.uk/pmr/page/59/
    17 Jan 2022: In short,getting out the data under reasonable conditions should be a routine part of the business of public administrations.”. ... Even when the data items are OKD-Open, the site is not necessarily so.
  21. #scholrev: Strategy and decentralisation | petermr's blog

    https://blogs.ch.cam.ac.uk/pmr/2013/03/24/scholrev-strategy-and-decentralisation/
    17 Jan 2022: The database would be available for bulk download and data mining. ... An open API is problematic if the data can’t be dumped.
  22. Library Workshop for virtual scholars | petermr's blog

    https://blogs.ch.cam.ac.uk/pmr/2008/06/25/library-workshop-for-virtual-scholars/
    17 Jan 2022: is the supplememtal data copyrighted? by whom? In some cases the answers are easy. ... Then we looked at the technology of scientific data. Download OSCAR/Experimental data checker from RSC site (Google for it – I deliberately don’t give URLs any more
  23. More clarification from Stevan Harnad | petermr's blog

    https://blogs.ch.cam.ac.uk/pmr/2008/05/04/more-clarification-from-stevan-harnad/
    17 Jan 2022: primarily research articles published in peer-reviewed journals. OA means that any user, anywhere, who has access to the Internet, may link, read, download, store, print-off, use, and data-mine ... It makes no mention of the re-use or re-publication of
  24. petermr's blog | A Scientist and the Web | Page 145

    https://blogs.ch.cam.ac.uk/pmr/page/145/
    17 Jan 2022: Pubchem holds links to the Chemspider compounds but does not actually hold the data. ... If Chemspider allows the direct download and re-use of their data from their site then I also congratulate them.
  25. Open API (or glorious API?) | petermr's blog

    https://blogs.ch.cam.ac.uk/pmr/2011/09/15/open-api-or-glorious-api/
    17 Jan 2022: data available for bulk download. That is a limitation we all regret. ... but there it is. I would argue that because the data we make.
  26. Can I data- and Text-mine Pubmed Central? | petermr's blog

    https://blogs.ch.cam.ac.uk/pmr/2008/04/05/can-i-data-and-text-mine-pubmed-central/
    17 Jan 2022: There is no explicit mention of the right to download material for data-mining and a lot of verbiage about “consistency with publishers’s policies” which is no help to scientists ... However, you can download download the entire Open Access subset
  27. Derivative use of Open Access works | petermr's blog

    https://blogs.ch.cam.ac.uk/pmr/2007/11/02/derivative-use-of-open-access-works/
    17 Jan 2022: data. I wish you luck resolving this so that we can access the data. ... The data distribution site does not need to be on the same machine as your service.
  28. petermr's blog | A Scientist and the Web | Page 132

    https://blogs.ch.cam.ac.uk/pmr/page/132/
    17 Jan 2022: There is no explicit mention of the right to download material for data-mining and a lot of verbiage about “consistency with publishers’s policies” which is no help to scientists ... So we have to embed the data capture directly into the laboratory.
  29. Open Access at the Royal Society of Chemistry | petermr's blog

    https://blogs.ch.cam.ac.uk/pmr/2008/05/16/open-access-at-the-royal-society-of-chemistry/
    17 Jan 2022: Because, publishers, the quality of your science depends in large part on the data related to those publications. ... And the chirality really is R- not S-“. But to make these claims the data must be free.
  30. https://blogs.ch.cam.ac.uk/pmr/category/data/feed/index.xml

    https://blogs.ch.cam.ac.uk/pmr/category/data/feed/index.xml
    17 Jan 2022: Pubchem holds links to the Chemspider compounds but does not actually hold the data. ... number of rotatable bonds) and names). It does, of course, hold the data that NIH collects through the roadmap program.
  31. petermr's blog | A Scientist and the Web | Page 118

    https://blogs.ch.cam.ac.uk/pmr/page/118/
    17 Jan 2022: USA). The data is all obtained by the scientific community and should be available without charge. ... Then we looked at the technology of scientific data. Download OSCAR/Experimental data checker from RSC site (Google for it – I deliberately don’t
  32. petermr's blog | A Scientist and the Web | Page 99

    https://blogs.ch.cam.ac.uk/pmr/page/99/
    17 Jan 2022: FF:We can mine the data from the PDF text. EW:Theoretically, yes. ... Under NPG’s terms of reuse, users may view, print, copy, download and text and data-mine the content for the purposes of academic research.
  33. petermr's blog | A Scientist and the Web | Page 82

    https://blogs.ch.cam.ac.uk/pmr/page/82/
    17 Jan 2022: The main data will come from patents, and I have been modifying David Jessop’s download and analyser so that they can be distributed. ... If the data had been openly available these errors would not have happened.
  34. How can we publish semantic chemical documents? | petermr's blog

    https://blogs.ch.cam.ac.uk/pmr/2009/03/16/how-can-we-publish-semantic-chemical-documents/
    17 Jan 2022: For those public studies people can download all the raw data and all the annotated and result data and even the underlying software. ... our experiments and download RAW and processed data and all needed software and that can only be topped by Open
  35. petermr's blog | A Scientist and the Web | Page 26

    https://blogs.ch.cam.ac.uk/pmr/page/26/
    17 Jan 2022: Amazing. Yesterday we had a huge [s]pike in the answers, and today all the data have been analyzed. ... Michael and his team now have to download the results, study them, and if they have more data add it to the system 🙂.
  36. Robots can detect error; but images MUST be Open | petermr's blog

    https://blogs.ch.cam.ac.uk/pmr/2008/05/29/robots-can-detect-error-but-images-must-be-open/
    17 Jan 2022: Simply, many researchers “doctor” their data. Not “most”, but “many”. The intent may be simply to make the data look “better” or they may be deliberately falsifying their data to obtain ... We will shan’t do this. We would download the
  37. petermr's blog | A Scientist and the Web | Page 91

    https://blogs.ch.cam.ac.uk/pmr/page/91/
    17 Jan 2022: Grant of Licence and Use of Data. You may print or download Content from the Service for your own personal use, provided that you keep intact all copyright and other proprietary ... Just click on the link while connected to the Internet to download the
  38. petermr's blog | A Scientist and the Web | Page 128

    https://blogs.ch.cam.ac.uk/pmr/page/128/
    17 Jan 2022: OA means that any user, anywhere, who has access to the Internet, may link, read, download, store, print-off, use, and data-mine the digital content of that article [PMR: without ... Or should there be more than one? We’ve got the data in.
  39. BiomedCentral use Open Data buttons in their publications |…

    https://blogs.ch.cam.ac.uk/pmr/2011/03/28/biomedcentral-use-open-data-buttons-in-their-publications/
    17 Jan 2022: See ourBy open data we mean that it is freely available on the public internet permitting any user to download, copy, analyse, re-process, pass them to software or use them ... This equates to a CC-BY, not a PDDL/CC0, licence but its effect is to make
  40. Proteomics: a community racing towards Open Data | petermr's blog

    https://blogs.ch.cam.ac.uk/pmr/2010/05/22/proteomics-a-community-racing-towards-open-data/
    17 Jan 2022: There is huge potential for re-using the data. This could be between species, cell types, diseases, etc. ... Because Tranche is part of the ProteomExchange consortium, however, other resources, such as PRIDE and Peptidome, have access to its data and
  41. petermr's blog | A Scientist and the Web | Page 122

    https://blogs.ch.cam.ac.uk/pmr/page/122/
    17 Jan 2022: about sequences and structures of biomolecules) the data are often more important than the fulltext. ... We will shan’t do this. We would download the articles, scan then for data and delete the articles.
  42. petermr's blog | A Scientist and the Web | Page 142

    https://blogs.ch.cam.ac.uk/pmr/page/142/
    17 Jan 2022: And what happens when you change the protocol? The data formats suddenly change. ... What I would really need is the digital raw data…preferably in some open format, which I can download, look at and work on.
  43. petermr's blog | A Scientist and the Web | Page 69

    https://blogs.ch.cam.ac.uk/pmr/page/69/
    17 Jan 2022: To answer you acid test: yes, you could download and mash up our data set in any way you see fit. ... The presence of John Wilbanks on the team. My acid test is” Can I systematically download all of the data in the Mendeley data base, transform it to
  44. petermr's blog | A Scientist and the Web | Page 188

    https://blogs.ch.cam.ac.uk/pmr/page/188/
    17 Jan 2022: These are truly excellent statistics if you consider that this is an open access system where people are depositing data, that these data are free to download and utilize even for ... The data in the literature can be awful – some measurements differ
  45. petermr's blog | A Scientist and the Web | Page 113

    https://blogs.ch.cam.ac.uk/pmr/page/113/
    17 Jan 2022: How can we help them to catch up? Can’t make it to Oxford on 2 April, I’m afraid – prior engagement – but I’ll download the proceedings. ... of going belly up under the NIH policy, but only when presented with the data to back it up.
  46. Availability of Crystallographic Data and Errors therein |…

    https://blogs.ch.cam.ac.uk/pmr/2008/06/22/availability-of-crystallographic-data-and-errors/
    17 Jan 2022: The IUCr has provided the CheckCIF service which is regularly used by authors to check the data for known problems. ... We have found that the data on CrystalEye are sufficient for many types of data-driven science.
  47. petermr's blog | A Scientist and the Web | Page 133

    https://blogs.ch.cam.ac.uk/pmr/page/133/
    17 Jan 2022: I could download one and within a minute[] OSCAR had read much of the chemical data from it. ... It changes the way we should capture and publish data. The Netherlands can justly feel proud in leading the world with the coherence and commitment of their
  48. petermr's blog | A Scientist and the Web | Page 66

    https://blogs.ch.cam.ac.uk/pmr/page/66/
    17 Jan 2022: Cambridge. What’s Open Data? By open data we mean that it is freely available on the public internet permitting any user to download, copy, analyse, re-process, pass them to ... Lensfield, a make facility for data. Download zipfile:.
  49. Mendeley, Scopus, Talis – will you be making your data Open? |…

    https://blogs.ch.cam.ac.uk/pmr/2010/08/27/mendeley-scopus-talis-will-you-be-making-your-data-open/
    17 Jan 2022: analysis of the data, especially from many fields, comes up with radical new insights. ... We must know that – in principle – we have the absolute right to download and re-purpose the data.
  50. FROG – not just Free, but Open (PRODRG take note) | petermr's blog

    https://blogs.ch.cam.ac.uk/pmr/2007/10/13/frog-not-just-free-but-open-prodrg-take-note/
    17 Jan 2022: May I download the data and use it in my own database(s)? ... I have attempted to clean up your judgments regarding the fact that Wiley are deriving their data from the literature.
  51. Open-Data-driven science and a brokering system for ONS |…

    https://blogs.ch.cam.ac.uk/pmr/2007/10/14/open-data-driven-science-and-a-brokering-system-for-ons/
    17 Jan 2022: Because the data is completely open I am not asking for people’s email addresses. ... Two people have commented so tonight I looked for the CrystalEye data to download but cannot find the download site.

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