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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

Data Details Chemical structures.
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Figure 9: Data Details Chemical structures.

Mentions: (Figure 9) So I go now into some details of the chemical structures we collected (Endnote 5). You can download an SDF file from us and say great I'll take my structures and go on. Here is all the stuff I have to deal with to get it to an SDF file. So in 1955 collecting chemical structures meant sort of ink drawings on 3 × 5 cards; that's the beginnings of our compound collection. In the 1970s there was this SANSS (Structure and nomenclature search system) which essentially was a connection table format. It gave you the atoms and which atoms were connected and what the bond order was but it had no coordinate information, no display information. This I think was partly due to CAS. There was also the EPA NIH chemical information system that was coming about here. For about twenty years starting about 1980 we had what we called the drug information system. The connection tables were stored in CAS but you also had a picture. The picture was stored in the database as HP plotter pen movement commands, so you can get a picture, you can get a connection table but you couldn't put them together at least in any useful way.


Adventures in public data.

Zaharevitz DW - J Cheminform (2011)

Data Details Chemical structures.
© Copyright Policy - open-access
Related In: Results  -  Collection

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

Figure 9: Data Details Chemical structures.
Mentions: (Figure 9) So I go now into some details of the chemical structures we collected (Endnote 5). You can download an SDF file from us and say great I'll take my structures and go on. Here is all the stuff I have to deal with to get it to an SDF file. So in 1955 collecting chemical structures meant sort of ink drawings on 3 × 5 cards; that's the beginnings of our compound collection. In the 1970s there was this SANSS (Structure and nomenclature search system) which essentially was a connection table format. It gave you the atoms and which atoms were connected and what the bond order was but it had no coordinate information, no display information. This I think was partly due to CAS. There was also the EPA NIH chemical information system that was coming about here. For about twenty years starting about 1980 we had what we called the drug information system. The connection tables were stored in CAS but you also had a picture. The picture was stored in the database as HP plotter pen movement commands, so you can get a picture, you can get a connection table but you couldn't put them together at least in any useful way.

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