Comments on: Defrosting the Digital Library http://duncan.hull.name/2008/10/31/defrosting-the-digital-library/ A personal laboratory notebook Thu, 11 Mar 2010 13:39:52 +0000 http://wordpress.com/ hourly 1 By: Defrosting the digital library at WoW! Wouter on the Web http://duncan.hull.name/2008/10/31/defrosting-the-digital-library/#comment-2147 Defrosting the digital library at WoW! Wouter on the Web Sat, 27 Dec 2008 13:23:20 +0000 http://dullhunk.wordpress.com/?p=928#comment-2147 [...] Duncan Hull, Steve R. Pettifer and Douglas B. Kell (2008) wrote an interesting review on the current state of personal digital libraries. It is perhaps important to stress the fact that in the end the review focused on personal digital libraries, where a lot can also be written on digital libraries at higher aggregation levels. But including those digital libraries at higher aggregation levels would take another review. Anyway, many of the observations for building personal digital libraries they describe are right and come straight from the workbench of the practicing systems biologist. But still some additional observations could have been addressed in this review as well. [...] [...] Duncan Hull, Steve R. Pettifer and Douglas B. Kell (2008) wrote an interesting review on the current state of personal digital libraries. It is perhaps important to stress the fact that in the end the review focused on personal digital libraries, where a lot can also be written on digital libraries at higher aggregation levels. But including those digital libraries at higher aggregation levels would take another review. Anyway, many of the observations for building personal digital libraries they describe are right and come straight from the workbench of the practicing systems biologist. But still some additional observations could have been addressed in this review as well. [...]

]]> By: Paulo Nuin http://duncan.hull.name/2008/10/31/defrosting-the-digital-library/#comment-1791 Paulo Nuin Sat, 01 Nov 2008 11:29:39 +0000 http://dullhunk.wordpress.com/?p=928#comment-1791 Congrats on the paper Duncan! Very nice, and timely. I will start a series of Bioinformatics and Informatics seminars in the department and the first one is about reference management. I will definitely use your paper and mention it. Cheers Paulo Congrats on the paper Duncan!

Very nice, and timely. I will start a series of Bioinformatics and Informatics seminars in the department and the first one is about reference management. I will definitely use your paper and mention it.

Cheers
Paulo

]]> By: Mikel Egaña http://duncan.hull.name/2008/10/31/defrosting-the-digital-library/#comment-1780 Mikel Egaña Fri, 31 Oct 2008 15:16:40 +0000 http://dullhunk.wordpress.com/?p=928#comment-1780 Very nice paper, congratulations! I especially agree with the bit on publishing models instead of papers. I really think that publishing some kind of expressive model (OWL ontologies???) that already links to other models at publication time is the key. The core publication would be the model, and the related paper supplementary material. So journals would be more like giant knowledge bases, linked to each other. Nice. For example, if my paper says that A phosphorilates B, I would publish a little ontology in OntoMedCentral stating that A phosphorilates B, of course importing A and B from uniprot and phosphorilates from the IntAct interactions ontology. In the same ontology, the paper would be codified in the annotations. A second paper says that as result of A phosphorilating B, I get cancer. The author of the second paper need only to link to the model I have just published, and so on. Mikel Very nice paper, congratulations!

I especially agree with the bit on publishing models instead of papers. I really think that publishing some kind of expressive model (OWL ontologies???) that already links to other models at publication time is the key. The core publication would be the model, and the related paper supplementary material. So journals would be more like giant knowledge bases, linked to each other. Nice.

For example, if my paper says that A phosphorilates B, I would publish a little ontology in OntoMedCentral stating that A phosphorilates B, of course importing A and B from uniprot and phosphorilates from the IntAct interactions ontology. In the same ontology, the paper would be codified in the annotations. A second paper says that as result of A phosphorilating B, I get cancer. The author of the second paper need only to link to the model I have just published, and so on.

Mikel

]]> By: Victor http://duncan.hull.name/2008/10/31/defrosting-the-digital-library/#comment-1777 Victor Fri, 31 Oct 2008 11:44:22 +0000 http://dullhunk.wordpress.com/?p=928#comment-1777 Thank you, Duncan - great review. I'm happy that you included Mendeley in it! May I just point to a minor inaccuracy in your description: By writing that Mendeley can only extract metadata from PDFs where it "is available in an amenable format" and by citing Howison & Goodrum, you seem to imply that Mendeley reads the PDF files' embedded metadata fields for its automatic document recognition. This is not the case: Mendeley doesn't rely on the embedded metadata fields, since (as Howison & Goodrum point out) they are usually empty. Instead, Mendeley extracts the full text of the document and, using regular expression and Hidden Markov Model algorithms, tries to "guess" the correct metadata based on the layout, formatting, and text. It's true, though, that the recognition quality is much better for journal articles formatted in a certain way (e.g. Elsevier, Kluwer, or Wiley journals) than for others. Improving this is one of our main development priorities in November/December. Cheers, Victor Thank you, Duncan – great review. I’m happy that you included Mendeley in it! May I just point to a minor inaccuracy in your description: By writing that Mendeley can only extract metadata from PDFs where it “is available in an amenable format” and by citing Howison & Goodrum, you seem to imply that Mendeley reads the PDF files’ embedded metadata fields for its automatic document recognition.

This is not the case: Mendeley doesn’t rely on the embedded metadata fields, since (as Howison & Goodrum point out) they are usually empty. Instead, Mendeley extracts the full text of the document and, using regular expression and Hidden Markov Model algorithms, tries to “guess” the correct metadata based on the layout, formatting, and text.

It’s true, though, that the recognition quality is much better for journal articles formatted in a certain way (e.g. Elsevier, Kluwer, or Wiley journals) than for others. Improving this is one of our main development priorities in November/December.

Cheers,
Victor

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