Limits...
Adventures in public data.

Zaharevitz DW - J Cheminform (2011)

Bottom Line: We, the Editors, wish to make clear however that this is an exception that we made because we would like to preserve the temporal unity and message of this set of publications.Insisting on a formal publication would have meant losing this historical account as part of the thematic series of papers or disrupting the series.We hope that this will find the consent of our readership.

View Article: PubMed Central - HTML - PubMed

Affiliation: National Cancer Institute/NIH, Bethesda, Maryland, USA. zaharevd@mail.nih.gov.

ABSTRACT
This article contains the slides and transcript of a talk given by Dan Zaharevitz at the "Visions of a Semantic Molecular Future" symposium held at the University of Cambridge Department of Chemistry on 2011-01-19. A recording of the talk is available on the University Computing Service's Streaming Media Service archive at http://sms.cam.ac.uk/media/1095515 (unfortunately the first part of the recording was corrupted, so the talk appears to begin at slide 6, 'At a critical time'). We believe that Dan's message comes over extremely well in the textual transcript and that it would be poorer for serious editing. In addition we have added some explanations and references of some of the concepts in the slides and text. (Charlotte Bolton; Peter Murray-Rust, University of Cambridge) EDITORIAL PREFACE: The following paper is part of a series of publications which arose from a Symposium held at the Unilever Centre for Molecular Informatics at the University of Cambridge to celebrate the lifetime achievements of Peter Murray-Rust. One of the motives of Peter's work was and is a better transport and preservation of data and information in scientific publications. In both respects the following publication is relevant: it is about public data and their representation, and the publication represents a non-standard experiment of transporting the content of the scientific presentation. As you will see, it consists of the original slides used by Dan Zaharevitz in his talk "Adventures in Public Data" at the Unilever Centre together with a diligent transcript of his speech. The transcribers have gone through great effort to preserve the original spirit of the talk by preserving colloquial language as it is used at such occasions. For reasons known to us, the original speaker was unable to submit the manuscript in a more conventional form. We, the Editors, have discussed in depth whether such a format is suitable for a scientific journal. We have eventually decided to publish this "as is". We did this mostly because it was Peter's wish that this talk was published in this form and because we agreed with his notion that this format transmits the message just as well as a formal article as defined by our instructions for authors. We, the Editors, wish to make clear however that this is an exception that we made because we would like to preserve the temporal unity and message of this set of publications. Insisting on a formal publication would have meant losing this historical account as part of the thematic series of papers or disrupting the series. We hope that this will find the consent of our readership.

No MeSH data available.


Related in: MedlinePlus

Structure release.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
getmorefigures.php?uid=PMC3198951&req=5

Figure 11: Structure release.

Mentions: (Figure 11) Structure release. The first one we put on the NIH page, not a page, just for anonymous FTP. I think it's generally called the NCI 127 k. They were open structures for which there was a CAS number. We figured the other thing to realise is that a lot of people say 'can you give us the chemical names of all these structures?' The vast majority of these structures were not published on, or at least we don't know that they were published on: no one ever bothered to name it, there's certainly not a trivial name. And so for a lot of the structures the only identifier we had was the NSC number and of course back in 1994 nobody knew what an NSC number was except for a handful of people interacting with NCI. We didn't think that was very useful so we sub selected a set where we also had the CAS numbers. Historical aside: CAS was our input contractor for about 6 or 8 years about 1975-1983 or something, so they automatically assigned a CAS number for everything that came in. And so there were CAS numbers: you figured you might be able to search on that and so that's where this group came from. Where we got the coordinates-it was actually the SANSS connection tables, they were converted to a SD format and the programme CORINA [1] from Johann Gasteiger was used to generate 3D coordinates, so that was the first stage of the release.


Adventures in public data.

Zaharevitz DW - J Cheminform (2011)

Structure release.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC3198951&req=5

Figure 11: Structure release.
Mentions: (Figure 11) Structure release. The first one we put on the NIH page, not a page, just for anonymous FTP. I think it's generally called the NCI 127 k. They were open structures for which there was a CAS number. We figured the other thing to realise is that a lot of people say 'can you give us the chemical names of all these structures?' The vast majority of these structures were not published on, or at least we don't know that they were published on: no one ever bothered to name it, there's certainly not a trivial name. And so for a lot of the structures the only identifier we had was the NSC number and of course back in 1994 nobody knew what an NSC number was except for a handful of people interacting with NCI. We didn't think that was very useful so we sub selected a set where we also had the CAS numbers. Historical aside: CAS was our input contractor for about 6 or 8 years about 1975-1983 or something, so they automatically assigned a CAS number for everything that came in. And so there were CAS numbers: you figured you might be able to search on that and so that's where this group came from. Where we got the coordinates-it was actually the SANSS connection tables, they were converted to a SD format and the programme CORINA [1] from Johann Gasteiger was used to generate 3D coordinates, so that was the first stage of the release.

Bottom Line: We, the Editors, wish to make clear however that this is an exception that we made because we would like to preserve the temporal unity and message of this set of publications.Insisting on a formal publication would have meant losing this historical account as part of the thematic series of papers or disrupting the series.We hope that this will find the consent of our readership.

View Article: PubMed Central - HTML - PubMed

Affiliation: National Cancer Institute/NIH, Bethesda, Maryland, USA. zaharevd@mail.nih.gov.

ABSTRACT
This article contains the slides and transcript of a talk given by Dan Zaharevitz at the "Visions of a Semantic Molecular Future" symposium held at the University of Cambridge Department of Chemistry on 2011-01-19. A recording of the talk is available on the University Computing Service's Streaming Media Service archive at http://sms.cam.ac.uk/media/1095515 (unfortunately the first part of the recording was corrupted, so the talk appears to begin at slide 6, 'At a critical time'). We believe that Dan's message comes over extremely well in the textual transcript and that it would be poorer for serious editing. In addition we have added some explanations and references of some of the concepts in the slides and text. (Charlotte Bolton; Peter Murray-Rust, University of Cambridge) EDITORIAL PREFACE: The following paper is part of a series of publications which arose from a Symposium held at the Unilever Centre for Molecular Informatics at the University of Cambridge to celebrate the lifetime achievements of Peter Murray-Rust. One of the motives of Peter's work was and is a better transport and preservation of data and information in scientific publications. In both respects the following publication is relevant: it is about public data and their representation, and the publication represents a non-standard experiment of transporting the content of the scientific presentation. As you will see, it consists of the original slides used by Dan Zaharevitz in his talk "Adventures in Public Data" at the Unilever Centre together with a diligent transcript of his speech. The transcribers have gone through great effort to preserve the original spirit of the talk by preserving colloquial language as it is used at such occasions. For reasons known to us, the original speaker was unable to submit the manuscript in a more conventional form. We, the Editors, have discussed in depth whether such a format is suitable for a scientific journal. We have eventually decided to publish this "as is". We did this mostly because it was Peter's wish that this talk was published in this form and because we agreed with his notion that this format transmits the message just as well as a formal article as defined by our instructions for authors. We, the Editors, wish to make clear however that this is an exception that we made because we would like to preserve the temporal unity and message of this set of publications. Insisting on a formal publication would have meant losing this historical account as part of the thematic series of papers or disrupting the series. We hope that this will find the consent of our readership.

No MeSH data available.


Related in: MedlinePlus