Calculating time from submission to publication / Degree of burden in submitting a paper

After "404 not found": a database of non-functional resources in the NAR database collection, I've uploaded my second dataset on figshare:
Calculating time from submission to publication / Degree of burden in submitting a paper.

Calculating time from submission to publication / Degree of burden in submitting a paper. Pierre Lindenbaum,  Ryan Delahanty.
figshare.
Retrieved  10:13, Oct 14, 2012 (GMT)
http://dx.doi.org/10.6084/m9.figshare.96403

This dataset was inspired by this post on biostar, initialy asked by Ryan Delahanty: I was wondering if it would be possible to calculate some kind of a metric for the speed-of-publication for each journal. I'm not sure submitted and accepted dates are available for all papers, but I noticed in XML data there are fields like the following:

<PubmedData>
        <History>
            <PubMedPubDate PubStatus="received">
                <Year>2011</Year>
                <Month>11</Month>
                <Day>29</Day>
                <Hour>6</Hour>
                <Minute>0</Minute>
            </PubMedPubDate>
            <PubMedPubDate PubStatus="accepted">
                <Year>2011</Year>
                <Month>12</Month>
                <Day>20</Day>
                <Hour>6</Hour>
                <Minute>0</Minute>
            </PubMedPubDate>
           (...)

In this dataset, the script 'pubmed.sh" downloads the the journals from http://www.ncbi.nlm.nih.gov/books/NBK3827/table/pubmedhelp.pubmedhelptable45/ , the 'eigenfactors' from http://www.eigenfactor.org.

For each journal , It scans pubmed (starting from year=2000) and get the difference between the date[@PubStatus='received'] and the date[@PubStatus='accepted'].

title	issn	eigenfactor	days
"Acta biochimica Polonica"	0001-527X	0.003996	119.770935960591
"Acta biomaterialia"	1742-7061	0.02152	129.682692307692
"Acta biotheoretica"	0001-5342	0.000844	161.897058823529
"Acta cirurgica brasileira / Sociedade Brasileira para Desenvolvimento Pesquisa em Cirurgia"	0102-8650	0.00128	122.038461538462
"Acta cytologica"	0001-5547	0.002305	65.3006134969325
"Acta diabetologica"	0940-5429	0.001851	299.6
"Acta haematologica"	0001-5792	0.002825	118.654676258993
"Acta histochemica"	0065-1281	0.002162	110.471204188482
"Acta histochemica et cytochemica"	0044-5991	0.000677	81.6455696202532
"Acta neurochirurgica"	0001-6268	0.009685	204.371830985916
"Acta neuropathologica"	0001-6322	0.023471	69.7277882797732
"Acta theriologica"	0001-7051	0.000901	147.0
"Acta tropica"	0001-706X	0.01011	196.577777777778
"Acta veterinaria Scandinavica"	0044-605X	0.001612	82.0
"Addictive behaviors"	0306-4603	0.017915	163.049731182796
"Advances in space research "	0273-1177	0.021217	205.0
Ambio	0044-7447	0.007463	181.878048780488
"American journal of human genetics"	0002-9297	0.120156	67.1898928024502
"American journal of hypertension"	0895-7061	0.017359	104.074576271186
(....)

Here is the kind of figure I got:

As far as I remember, "Cell" is the point having the highest eigenfactor.


Note: pubmed contains some errors: e.g. received > accepted (http://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=pubmed&id=20591334&retmode=xml) or some dates in the future: ( http://eutils.ncbi.nlm.nih.gov/entrez/eutils/efetch.fcgi?db=pubmed&id=12921703&retmode=xml )


That's it,

Pierre

A new journal: BMC Open Research Computation #OpenResComp

www.openresearchcomputation.com

Citing ''Aims & scope'':Open Research Computation publishes peer reviewed articles that describe the development, capacities, and uses of software designed for use by researchers in any field.

Submissions relating to software for use in any area of research are welcome as are articles dealing with algorithms, useful code snippets, as well as large applications or web services, and libraries.

Open Research Computation differs from other journals with a software focus in its requirement for the software source code to be made available under an Open Source Initiative compliant license, and in its assessment of the quality of documentation and testing of the software.

In addition to articles describing software Open Research Computation also welcomes submissions that review or describe developments relating to software based tools for research. These include, but are not limited to, reviews or proposals for standards, discussion of best practice in research software development, educational and support resources and tools for researchers that develop or use software based tools.

See also the insights from Cameron Neylon, Jan Aerts, Neil 10K Saunders ...

Learning OWL: a simple Ontology for contributions

This post is a simple reminder for creating a simple OWL ontology, I know RDFS (RDF schema) but I'm not at all an expert with the OWL language, so feel free to make any comment about the following ontology.

OK...

at the beginning there is an empty RDF document:

<?xml version="1.0" encoding="ISO-8859-1"?>
<!DOCTYPE rdf:RDF [
<!ENTITY rdf "http://www.w3.org/1999/02/22-rdf-syntax-ns#">
]>
<rdf:RDF xmlns:rdf="&rdf;">
</rdf:RDF>

We're going to use a few more namespaces:

• DC: the Dublin core provides the basic metadata to describe a resource (title, author...)
• RDFS: the namespace for the simpliest RDF ontology
• OWL a more precise language for describing an ontology extendings RDFs
• FOAF. defines the People, the Images, the Documents, etc...
• biogang: this will be the prefix for our ontology

<?xml version="1.0" encoding="ISO-8859-1"?>
<!DOCTYPE rdf:RDF [
<!ENTITY rdf "http://www.w3.org/1999/02/22-rdf-syntax-ns#">
<!ENTITY rdfs "http://www.w3.org/2000/01/rdf-schema#">
<!ENTITY owl "http://www.w3.org/2002/07/owl#">
<!ENTITY dc "http://purl.org/dc/elements/1.1/">
<!ENTITY biogang "urn:biogang/ontology/contribution#">
<!ENTITY foaf "http://xmlns.com/foaf/0.1/">
]>
<rdf:RDF xmlns:rdf="&rdf;"
xmlns:rdfs="&rdfs;"
xmlns:owl="&owl;"
xmlns:foaf="&foaf;"
xmlns:dc="&dc;"
xmlns:biogang="&biogang;">

</rdf:RDF>

In a first statement We describe our Ontology (label, comment,...)

<?xml version="1.0" encoding="ISO-8859-1"?>
<!DOCTYPE rdf:RDF [
<!ENTITY rdf "http://www.w3.org/1999/02/22-rdf-syntax-ns#">
<!ENTITY rdfs "http://www.w3.org/2000/01/rdf-schema#">
<!ENTITY owl "http://www.w3.org/2002/07/owl#">
<!ENTITY dc "http://purl.org/dc/elements/1.1/">
<!ENTITY foaf "http://xmlns.com/foaf/0.1/">
<!ENTITY biogang "urn:biogang/ontology/contribution#">
]>
<rdf:RDF xmlns:rdf="&rdf;" xmlns:rdfs="&rdfs;" xmlns:owl="&owl;" xmlns:dc="&dc;" xmlns:foaf="&foaf;" xmlns:biogang="&biogang;">

<owl:Ontology rdf:about="">
<dc:date>2009-06-11</dc:date>
<dc:creator>Pierre Lindenbaum</dc:creator>
<rdfs:label>The Attribution Ontology</rdfs:label>
<rdfs:comment>
An ontology used to provide a quantitative citation
for every unique author of a document
</rdfs:comment>
</owl:Ontology>
</rdf:RDF>

Let's declare our main class, an Attribution:

<owl:Class rdf:about="&biogang;Contribution">
<rdfs:label xml:lang="en">Contribution</rdfs:label>
<rdfs:label xml:lang="fr">Contribution</rdfs:label>
<rdfs:comment xml:lang="en">A contribution</rdfs:comment>
<rdfs:comment xml:lang="fr">Une contribution</rdfs:comment>
</owl:Class>

An attribution is a link between an author and a document.
An author is a foaf:Person as defined in the FOAF ontology.
A document is a foaf:Document as defined in the FOAF ontology (this could be an article but also a picture, a song, a web site, etc...).
So, an Attribution is a Class with two properties: contributor and contributedTo.
The domain of both contributor and contributedTo is an object of type Contribution.
The range of a "contributor" is NOT the name of the author (aka a Literal, aka a DataTypeProperty) but it is a link to a resource describing the Person. So its range is an ObjectProperty pointing to a foaf:Person. Also contributedTo extends the Dublin-Core property dc:creator

<owl:ObjectProperty rdf:about="&biogang;contributor">
<rdfs:domain rdf:resource="&biogang;Contribution"/>
<rdfs:range rdf:resource="&foaf;Person"/>
<rdfs:label>contributor</rdfs:label>
<rdfs:subPropertyOf rdf:resource="&dc;creator"/>
</owl:ObjectProperty>

The range of contributedTo" is NOT the literal description of the document but it is a link to a resource describing the Document. So its range is an ObjectProperty pointing to a foaf:Document.

<owl:ObjectProperty rdf:about="&biogang;contributedTo">
<rdfs:domain rdf:resource="&biogang;Contribution"/>
<rdfs:range rdf:resource="&foaf;Document"/>
<rdfs:label>contributed to</rdfs:label>
</owl:ObjectProperty>

We can also add a Literal property to describe the nature of the contribution.

<owl:DatatypeProperty rdf:about="&biogang;comment">
<rdfs:domain rdf:resource="&biogang;Contribution"/>
<rdfs:range rdf:resource="&rdfs;Literal"/>
<rdfs:label>description of this contribution</rdfs:label>
<rdfs:subPropertyOf rdf:resource="&dc;description"/>
</owl:DatatypeProperty>

But a Contribution should contain one 'contributor' and one 'contributedTo', so we add a restriction on the cardinality of those properties:

<owl:Class rdf:about="&biogang;Contribution">
<rdfs:label xml:lang="en">Contribution</rdfs:label>
<rdfs:label xml:lang="fr">Contribution</rdfs:label>
<rdfs:comment xml:lang="en">A contribution</rdfs:comment>
<rdfs:comment xml:lang="fr">Une contribution</rdfs:comment>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="&biogang;contributor"/>
<owl:cardinality rdf:datatype="http://www.w3.org/2001/XMLSchema#nonNegativeInteger">1</owl:cardinality>
</owl:Restriction>
</rdfs:subClassOf>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="&biogang;contributedTo"/>
<owl:cardinality rdf:datatype="http://www.w3.org/2001/XMLSchema#nonNegativeInteger">1</owl:cardinality>
</owl:Restriction>
</rdfs:subClassOf>
</owl:Class>

We can also create a set of sub-Classes to extend the Class Contribution to give a quantifiable view of the contribution.

<owl:Class rdf:about="&biogang;MajorContribution">
<rdfs:subClassOf rdf:resource="&biogang;Contribution"/>
<rdfs:label>Major contribution</rdfs:label>
</owl:Class>

<owl:Class rdf:about="&biogang;MediumContribution">
<rdfs:subClassOf rdf:resource="&biogang;Contribution"/>
<rdfs:label>Medium contribution</rdfs:label>
</owl:Class>

<owl:Class rdf:about="&biogang;MicroContribution">
<rdfs:subClassOf rdf:resource="&biogang;Contribution"/>
<rdfs:label>Micro contribution</rdfs:label>
</owl:Class>

It would be also nice, to extends this ontology to describe the 'nature' of the contribution (drawing figures, useful discussions, writing the paper). This would allow to easily find the person who are good with a given task.
Anyway, at the end, here is the full ontology:

<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:rdfs="http://www.w3.org/2000/01/rdf-schema#" xmlns:owl="http://www.w3.org/2002/07/owl#" xmlns:dc="http://purl.org/dc/elements/1.1/" xmlns:biogang="urn:biogang/ontology/contribution#">

<owl:Ontology rdf:about="">
<dc:date>2009-06-11</dc:date>
<dc:creator>Pierre Lindenbaum</dc:creator>
<rdfs:label>The Attribution Ontology</rdfs:label>
<rdfs:comment>
An ontology used to provide a quantitative citation
for every unique author of a document
</rdfs:comment>
</owl:Ontology>

<owl:Class rdf:about="urn:biogang/ontology/contribution#Contribution">
<rdfs:label xml:lang="en">Contribution</rdfs:label>
<rdfs:label xml:lang="fr">Contribution</rdfs:label>
<rdfs:comment xml:lang="en">A contribution</rdfs:comment>
<rdfs:comment xml:lang="fr">Une contribution</rdfs:comment>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="urn:biogang/ontology/contribution#contributor"/>
<owl:cardinality rdf:datatype="http://www.w3.org/2001/XMLSchema#nonNegativeInteger">1</owl:cardinality>
</owl:Restriction>
</rdfs:subClassOf>
<rdfs:subClassOf>
<owl:Restriction>
<owl:onProperty rdf:resource="urn:biogang/ontology/contribution#contributedTo"/>
<owl:cardinality rdf:datatype="http://www.w3.org/2001/XMLSchema#nonNegativeInteger">1</owl:cardinality>
</owl:Restriction>
</rdfs:subClassOf>
</owl:Class>


<owl:ObjectProperty rdf:about="urn:biogang/ontology/contribution#contributor">
<rdfs:domain rdf:resource="urn:biogang/ontology/contribution#Contribution"/>
<rdfs:range rdf:resource="http://xmlns.com/foaf/0.1/Person"/>
<rdfs:label>contributor</rdfs:label>
<rdfs:subPropertyOf rdf:resource="http://purl.org/dc/elements/1.1/creator"/>
</owl:ObjectProperty>

<owl:ObjectProperty rdf:about="urn:biogang/ontology/contribution#contributedTo">
<rdfs:domain rdf:resource="urn:biogang/ontology/contribution#Contribution"/>
<rdfs:range rdf:resource="http://xmlns.com/foaf/0.1/Document"/>
<rdfs:label>contributed to</rdfs:label>
</owl:ObjectProperty>

<owl:DatatypeProperty rdf:about="urn:biogang/ontology/contribution#comment">
<rdfs:domain rdf:resource="urn:biogang/ontology/contribution#Contribution"/>
<rdfs:range rdf:resource="http://www.w3.org/2000/01/rdf-schema#Literal"/>
<rdfs:label>description of this contribution</rdfs:label>
<rdfs:subPropertyOf rdf:resource="http://purl.org/dc/elements/1.1/description"/>
</owl:DatatypeProperty>

<owl:Class rdf:about="urn:biogang/ontology/contribution#MajorContribution">
<rdfs:subClassOf rdf:resource="urn:biogang/ontology/contribution#Contribution"/>
<rdfs:label>Major contribution</rdfs:label>
</owl:Class>

<owl:Class rdf:about="urn:biogang/ontology/contribution#MediumContribution">
<rdfs:subClassOf rdf:resource="urn:biogang/ontology/contribution#Contribution"/>
<rdfs:label>Medium contribution</rdfs:label>
</owl:Class>

<owl:Class rdf:about="urn:biogang/ontology/contribution#MicroContribution">
<rdfs:subClassOf rdf:resource="urn:biogang/ontology/contribution#Contribution"/>
<rdfs:label>Micro contribution</rdfs:label>
</owl:Class>

</rdf:RDF>

At the end, we can create some new instances of contributions just like this:

<rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#" xmlns:biogang="urn:biogang/ontology/contribution#" (...) >
<biogang:MajorContribution>
<biogang:comment>Made the Y2H experiments</biogang:comment>
<biogang:contributor rdf:resource="mailto:plindenbaum@yahoo.fr"/>
<biogang:contributedTo rdf:resource="http://www.ncbi.nlm.nih.gov/pubmed/8985320"/>
</biogang:MajorContribution>

<foaf:Person rdf:about="mailto:plindenbaum@yahoo.fr">
<foaf:name>Pierre</foaf:name>
</foaf:Person>

<foaf:Document rdf:about="http://www.ncbi.nlm.nih.gov/pubmed/8985320">
<dc:title>In vivo and in vitro phosphorylation of rotavirus NSP5 correlates with its localization in viroplasms</dc:title>
</foaf:Document>
</rdf:RDF>

That's it
Pierre

Pubmed, impact factors, sorting and FriendFeed

I recently said on twitter that I wished I could sort the articles on pubmed using the impact factors of the journals. What followed was a demonstration of the power of friendfeed and was also observed under some other circumstances by Deepak Singh, Pedro Beltrao and some others... Within a day several persons joined the conversation on friendfeed and among them, Lars Juhl Jensen and Deepak suggested me to have a look at http://www.eigenfactor.org where the Eigenfactor is a measure of the journal's total importance to the scientific community. I must also cite Euan who was inspired by this discussion and created PubmedFaceoff, a photorealistic variant of the Chernoff Faces visualization technique based on pubmed.

Now let's go back to my sorting problem: I've joined the data from www.eigenfactor.org (with the kind permission of Carl Bergstrom) and from http://www.ncbi.nlm.nih.gov/entrez/citmatch_help.html#JournalLists and I've uploaded this new dataset on IBM-ManyEyes:

http://services.alphaworks.ibm.com/manyeyes/data
(You can play with this)

I wrote a java program reading a set of pubmed articles formatted in XML and using the scoring dataset. The algorithm is trivial: the XML element of the articles are removed from their parent node, sorted on their 'eigenfactors' retrieved from the journal <NlmId>, and then inserted back.

The source is available here

http://code.google.com

The executable jar (containing the scoring dataset) is available here:

http://lindenb.googlecode.com/files/sortpubmed.jar

Here is an example: I want to sort the articles about Charles Darwin. I've feched all the 372 articles in XML from this query

java -jar lindenb/build/sortpubmed.jar ~/pubmed_result.txt > result.xml

Here are the first articles:

    * Schmidhuber, Jürgen (Apr. 2008). "Comparing the legacies of Gauss, Pasteur and Darwin". Nature 452 (7187): 530. doi:10.1038/452530b. PMID 18256649. 
    * Padian, Kevin (Feb. 2008). "Darwin's enduring legacy". Nature 451 (7179): 632-4. doi:10.1038/451632a. PMID 18305520. 
    * Odling-Smee, Lucy (Mar. 2007). "Darwin and the 20-year publication gap". Nature 446 (7135): 478-9. doi:10.1038/446478a. PMID 17392756. 
    * Oliveira, João Gama; Barabási Albert-László (Oct. 2005). "Human dynamics: Darwin and Einstein correspondence patterns". Nature 437 (7063): 1251. doi:10.1038/4371251a. PMID 16724015. 
    * Kohn, David; Murrell Gina, Parker John, Whitehorn Mark (Aug. 2005). "What Henslow taught Darwin". Nature 436 (7051): 643-5. doi:10.1038/436643a. PMID 16079834. 
    * Ridley, Matt (Sep. 2004). "Crick and Darwin's shared publication in Nature". Nature 431 (7006): 244. doi:10.1038/431244a. PMID 15372004. 
    * Gruber, J W (Oct. 2001). "Owen was right, as Darwin's work continues". Nature 413 (6857): 669. doi:10.1038/35099725. PMID 11449244. 
    * Padian, K (Jul. 2001). "Owen's Parthian shot". Nature 412 (6843): 123-4. doi:10.1038/35084289. PMID 11606991. 
    * Rhodes, F H (. 1983). "Gradualism, punctuated equilibrium and the Origin of Species". Nature 305 (5932): 269-72. PMID 6353241. 
    * Maynard-Smith, J (Apr. 1982). "The century since Darwin". Nature 296 (5858): 599-601. PMID 7040979. 
    * "Darwin's questions" (Jan. 1969). Nature 221 (5178): 313. PMID 4884839. 
    * Hector, Andy; Hooper Rowan (Jan. 2002). "Ecology. Darwin and the first ecological experiment". Science 295 (5555): 639-40. doi:10.1126/science.1064815. PMID 11809960. 
    * Corsi (May. 1987). "Further Letters of Darwin: The Correspondence of Charles Darwin". Science 236 (4804): 988-989. doi:10.1126/science.236.4804.988. PMID 17812771. 
    * Schweber (May. 1985). "Darwin's Earliest Letters: The Correspondence of Charles Darwin". Science 228 (4701): 838-841. doi:10.1126/science.228.4701.838. PMID 17815024. 
    * Lewin, R (Aug. 1982). "Darwin died at a most propitious time". Science 217 (4561): 717-8. PMID 7048528. 
    * Gould, S J (Apr. 1982). "Darwinism and the expansion of evolutionary theory". Science 216 (4544): 380-7. PMID 7041256. 
    * Zirkle (May. 1964). "Charles Darwin". Science 144 (3619): 724-725. doi:10.1126/science.144.3619.724-a. PMID 17807061. 
    * Cholodny (Nov. 1937). "CHARLES DARWIN AND THE MODERN THEORY OF TROPISMS". Science 86 (2238): 468. doi:10.1126/science.86.2238.468. PMID 17815459. 
    * Leidy (Sep. 1929). "CEREMONY ATTENDING THE OPENING OF DOWN HOUSE, THE HOME OF CHARLES DARWIN". Science 70 (1810): 228-231. doi:10.1126/science.70.1810.228. PMID 17775389. 
    * Osborn (Jun. 1929). "GIFT TO DOWN HOUSE OF THE ORIGINAL LETTERS OF CHARLES DARWIN TO FRITZ MULLER". Science 69 (1799): 645. doi:10.1126/science.69.1799.645. PMID 17791947. 
    * Osborn (Dec. 1926). "A CONTEMPORARY OF CHARLES DARWIN". Science 64 (1669): 623-624. doi:10.1126/science.64.1669.623-a. PMID 17834475. 
    * Sampson (Sep. 1909). "LETTERS FROM CHARLES DARWIN". Science 30 (766): 303-304. doi:10.1126/science.30.766.303. PMID 17837456. 
    * Ayala, Francisco J (May. 2007). "Darwin's greatest discovery: design without designer". Proc. Natl. Acad. Sci. U.S.A. 104 Suppl 1: 8567-73. doi:10.1073/pnas.0701072104. PMID 17494753.

Thomson scientific launches www.researcherid.com

http://www.researcherid.com

Thomson scientific launches researcher id.com to associate a researcher with their published works:

Unique Identifier Ensures An Accurate Record Of A Researcher’s Output And Attribution and Builds a World-class Author Community

Researcher ID is a global, multi-disciplinary scholarly research community. Each researcher listed is assigned a unique identifier, to aid in solving the common problem of author misidentification. Search the registry to find citations, collaborators, and more.

see also: http://scientific.thomson.com/press/2008/8429910/

Pierre

Publish or Perish

FYI: Found today but not tested:


Publish or Perish - A citation analysis software program, designed to help individual academics to present their case for research impact to its best advantage.



Publish or Perish is a software program that retrieves and analyzes academic citations. It uses Google Scholar to obtain the raw citations, then analyzes these and presents the following statistics:

• Total number of papers


• Total number of citations


• Average number of citations per paper


• Average number of citations per author


• Average number of papers per author


• Average number of citations per year


• Hirsch's h-index and related parameters


• Egghe's g-index


• The contemporary h-index


• The age-weighted citation rate


• Two variations of individual h-indices


• An analysis of the number of authors per paper.

Bioinformatics as a Recreation

How can I find a laboratory looking for a small but useful piece of software I would write after work instead of loosing my time in watching TV ? I promise, I just want my name at the 876th position in the authors list :-)

Papiers Aléatoire

I'm starting a new blog called "Papier Aléatoires" (Random Papers). It will contain translations of abstracts in French in order to motivate myself to read more papers and to better understand them (this is my defect: I don't know how to identify a good article: as an example, I remember years ago I read the abstract of THIS paper introducing the siRNA without being interested). Nevertheless I am not certain that I will contribute to this blog on a regular basis.

Contributions are also welcomed: I'll post any french translation of any scholar abstract.
In the future, I may also store the translation in a public (RDF?) file.

Pierre

Nature Scintilla

just like Deepak, I've received an invitation from Euan Adie (thanks Euan) to join the new service from Nature http://scintilla.nature.com/.

Scintilla collects data from hundreds of news outlets, scientific blogs, journals and databases and then makes it easy for you to organize, share and discover exactly the type of information that you're interested in.

For example, you can keep track of life science podcasts, or the latest papers on schizophrenia, DNA methylation or immunology. Interested in physics blogs? Scintilla can help.

Euan is already the author of www.postgenomic.com and the two tools seem to have an identical function at first glance. This also reminds me Aggademia, a tool created and tested by Alf Eaton a year ago.

I just had on overview of this tool but I already I found it interesting to add a pubmed query in my collection of sources. The service is distinct from Connotea and network.nature.com but with those three tools you can create a group, send some invitations (people around me are annoyed with all my invitations) and I hope all of this will be merged in the future.

Shall I use this tool ? I don't know. I already use google-reader , technorati , etc.. to handles my resources, just tell me why I should change.

Science Magazine ? Science Magazine ? Where are you ?


Pierre

Is there any XMP in scientific pdf ? (No)

Roderic Page from iPhylo has introduced XMP in his blog. XMP is an Adobe format used to store metadata in files, such as PDFs. Adobe also provides an API to extract the XMP from the files.

I've downloaded the toolkit to see if any meta information could be extracted from the scientific papers. The adobe toolkit needs expat (a XML parser) to be installed and it comes with a sample application 'DumpScannedXMP' finding all XMP Packets in a file and printing their content.

I've tested this with some papers found on the net.
./target/i80386linux/debug/DumpScannedXMP 3851.pdf
RoXaN, a Novel Cellular Protein Containing TPR, LD, and Zinc Finger Motifs, Forms a Ternary Complex with Eukaryotic Initiation Factor 4G and Rotavirus NSP3: from Journal of Virology 2003

// ==============================================================

// Dumping raw input for "/home/pierre/3851.pdf" (879724..881254)

<?xpacket begin="" id="W5M0MpCehiHzreSzNTczkc9d"?>
<x:xmpmeta xmlns:x="adobe:ns:meta/" x:xmptk="3.1-701">
   <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
      <rdf:Description rdf:about=""
            xmlns:xap="http://ns.adobe.com/xap/1.0/">
         <xap:CreateDate>2004-03-16T15:35:47Z</xap:CreateDate>
         <xap:CreatorTool>XPP</xap:CreatorTool>
         <xap:ModifyDate>2007-05-22T12:24:37Z</xap:ModifyDate>
      </rdf:Description>
      <rdf:Description rdf:about=""
            xmlns:dc="http://purl.org/dc/elements/1.1/">
         <dc:format>application/pdf</dc:format>
         <dc:description>
            <rdf:Alt>
               <rdf:li xml:lang="x-default"/>
            </rdf:Alt>
         </dc:description>
         <dc:creator>
            <rdf:Seq>
               <rdf:li/>
            </rdf:Seq>
         </dc:creator>
         <dc:title>
            <rdf:Alt>
               <rdf:li xml:lang="x-default"/>
            </rdf:Alt>
         </dc:title>
      </rdf:Description>
      <rdf:Description rdf:about=""
            xmlns:pdf="http://ns.adobe.com/pdf/1.3/">
         <pdf:Keywords/>
         <pdf:Producer/>
      </rdf:Description>
      <rdf:Description rdf:about=""
            xmlns:xapMM="http://ns.adobe.com/xap/1.0/mm/">
         <xapMM:DocumentID>uuid:e0500da6-1dd1-11b2-0a00-ecd00f090858</xapMM:DocumentID>
         <xapMM:InstanceID>uuid:e0500db1-1dd1-11b2-0a00-000000004869</xapMM:InstanceID>
      </rdf:Description>
   </rdf:RDF>
</x:xmpmeta>
<?xpacket end="r"?>

Dumping XMPMeta object ""  (0x0)

   http://ns.adobe.com/xap/1.0/  xap:  (0x80000000 : schema)
      xap:CreateDate = "2004-03-16T15:35:47Z"
      xap:CreatorTool = "XPP"
      xap:ModifyDate = "2007-05-22T12:24:37Z"

   http://purl.org/dc/elements/1.1/  dc:  (0x80000000 : schema)
      dc:format = "application/pdf"
      dc:description  (0x1E00 : isLangAlt isAlt isOrdered isArray)
         [1] = ""  (0x50 : hasLang hasQual)
               ? xml:lang = "x-default"  (0x20 : isQual)
      dc:creator  (0x600 : isOrdered isArray)
         [1] = ""
      dc:title  (0x1E00 : isLangAlt isAlt isOrdered isArray)
         [1] = ""  (0x50 : hasLang hasQual)
               ? xml:lang = "x-default"  (0x20 : isQual)

   http://ns.adobe.com/pdf/1.3/  pdf:  (0x80000000 : schema)
      pdf:Keywords = ""
      pdf:Producer = ""

   http://ns.adobe.com/xap/1.0/mm/  xapMM:  (0x80000000 : schema)
      xapMM:DocumentID = "uuid:e0500da6-1dd1-11b2-0a00-ecd00f090858"
      xapMM:InstanceID = "uuid:e0500db1-1dd1-11b2-0a00-000000004869"

Pretty serialization, 1478 bytes :

<x:xmpmeta xmlns:x="adobe:ns:meta/" x:xmptk="Public XMP Toolkit Core 3.5">
   <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
      <rdf:Description rdf:about=""
            xmlns:xap="http://ns.adobe.com/xap/1.0/">
         <xap:CreateDate>2004-03-16T15:35:47Z</xap:CreateDate>
         <xap:CreatorTool>XPP</xap:CreatorTool>
         <xap:ModifyDate>2007-05-22T12:24:37Z</xap:ModifyDate>
      </rdf:Description>
      <rdf:Description rdf:about=""
            xmlns:dc="http://purl.org/dc/elements/1.1/">
         <dc:format>application/pdf</dc:format>
         <dc:description>
            <rdf:Alt>
               <rdf:li xml:lang="x-default"/>
            </rdf:Alt>
         </dc:description>
         <dc:creator>
            <rdf:Seq>
               <rdf:li/>
            </rdf:Seq>
         </dc:creator>
         <dc:title>
            <rdf:Alt>
               <rdf:li xml:lang="x-default"/>
            </rdf:Alt>
         </dc:title>
      </rdf:Description>
      <rdf:Description rdf:about=""
            xmlns:pdf="http://ns.adobe.com/pdf/1.3/">
         <pdf:Keywords/>
         <pdf:Producer/>
      </rdf:Description>
      <rdf:Description rdf:about=""
            xmlns:xapMM="http://ns.adobe.com/xap/1.0/mm/">
         <xapMM:DocumentID>uuid:e0500da6-1dd1-11b2-0a00-ecd00f090858</xapMM:DocumentID>
         <xapMM:InstanceID>uuid:e0500db1-1dd1-11b2-0a00-000000004869</xapMM:InstanceID>
      </rdf:Description>
   </rdf:RDF>
</x:xmpmeta>

Compact serialization, 990 bytes :

<x:xmpmeta xmlns:x="adobe:ns:meta/" x:xmptk="Public XMP Toolkit Core 3.5">
 <rdf:RDF xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#">
  <rdf:Description rdf:about=""
    xmlns:xap="http://ns.adobe.com/xap/1.0/"
    xmlns:dc="http://purl.org/dc/elements/1.1/"
    xmlns:pdf="http://ns.adobe.com/pdf/1.3/"
    xmlns:xapMM="http://ns.adobe.com/xap/1.0/mm/"
   xap:CreateDate="2004-03-16T15:35:47Z"
   xap:CreatorTool="XPP"
   xap:ModifyDate="2007-05-22T12:24:37Z"
   dc:format="application/pdf"
   pdf:Keywords=""
   pdf:Producer=""
   xapMM:DocumentID="uuid:e0500da6-1dd1-11b2-0a00-ecd00f090858"
   xapMM:InstanceID="uuid:e0500db1-1dd1-11b2-0a00-000000004869">
   <dc:description>
    <rdf:Alt>
     <rdf:li xml:lang="x-default"/>
    </rdf:Alt>
   </dc:description>
   <dc:creator>
    <rdf:Seq>
     <rdf:li/>
    </rdf:Seq>
   </dc:creator>
   <dc:title>
    <rdf:Alt>
     <rdf:li xml:lang="x-default"/>
    </rdf:Alt>
   </dc:title>
  </rdf:Description>
 </rdf:RDF>
</x:xmpmeta>

A test with a more recent paper RNAmmer: consistent and rapid annotation of ribosomal RNA genes . NAR 2007 contains as much information.

So is there any interesting XMP in scientific pdf ? no.


Pierre

Health Care, Life Sciences and the Semantic Web: Publication

From the W3C:

The Semantic Web Health Care and Life Sciences Interest Group (HCLSIG) has reached a significant milestone with their publication of the article "Advancing Translational Research with the Semantic Web." This joint work of the Interest Group was published in BMC Bioinformatics, a peer-reviewed open access journal that plays a central role in the bioinformatics community. The authors illustrate the value of Semantic Web technologies to neuroscience researchers and biomedicine and report on several projects by members of the Interest Group.

New Journal: Human Frontier Science Program Journal

The HFSP Journal aims to publish high quality, innovative interdisciplinary basic research at the frontier of biology over a wide range of organizational levels (from the molecular level to population biology) using principles strategies or technologies from the more quantitative disciplines (e.g. physics, chemistry, mathematics, engineering, or informatics).

http://hfspj.aip.org/