RDF for PubMedCentral

Editor's Notes

• #4: Not limited to open access modelsNot limited to closed business models
• #5: In spite of the advances, scientific publications remain poorly connected to each other as well as to external resources. Furthermore, most of the information remains locked up in discrete documents without machine-processable content.
• #6: 3rd point : As easy as building mash-ups
• #7: 4th point then The paper becomes an
• #13: Distribution of the first 20 journals, corresponding to about 40% of the total of 270,834 Number of biological entities identified across the papers
• #15: SPARQL queries can be used to retrieve metadata and content. It is possible to specify words and sentences that should appear in the text or in the section title.
• #16: As content has been semantically enriched, it is possible to retrieve articles based on either the annotated terms, e.g., “mixture,” or their corresponding biological entities, e.g., CHEBI:60004.
• #20: Users search for a human gene names; the term is initially resolved against GeneWiki, the associated UniProt accession is then used in the SPARQL query. The resulting set includes publication metadata, abstract, and a cloud of annotations. b) Enriched content based on annotations is displayed on the interactive zone; this may be the annotated paragraph, a chemical entity, or protein related information and so on.
• #21: Graph-based retrieval for the terms “catalase”; only shared terms with more than 30 associated biological terms are included in the results. We want to visualoize the network of interconected documents. How is a document related to another document, what do they share.
• #22: What are the challenges we have face so far in the PMC rdfication case? Well a first challenge is related to content, tables and images are not part of the core RDF but are referenced as links so we still have access to them. However, there are some inline tables whose files and columns are described in XML; so far we recover the content but not the format so we are missing information there. The supplementary material is still difficult to integrate, it could be a Section, another paper, a technical report following a total different schema, can be outside PMC, can be a footnote... Also, most of the documents follow the same schema, but we have found some few with a different one, those cannot be currently processed. Those cases are less than the 5%.As for the references, we have at least 4 different styles, so the process is different in each case and some times we get references that are just plain text so we have to do some extra process in order to get the metadata associated.And the annotators, well, they are web services so they can be down, or too busy. Also, the stop words are tricky, we have tried to avoid them as much as possible but it is always possible to get some noisy terms in the annotations.Nota: stop words son palabrascomo “they” “can” que son evitadaspor los anotadorespor ser muycomunes o muycortas. Peroesdifícilcubrirlastodas, tenemoslasmáscomunes. Otracuestiónesquepuede ser queperdamosinformaciónporquealgunosacrónimospuede ser iguales a un stop word. Porejemplo CAN es un acrónimousado en CHEBI perocomoesunapalabracomún la evitamos, si en algún paper CAN esusado en el contexto de CHEBI y no del verboauxiliar, estaríamosperdiendoesainformación.
• #30: Methods&materials, what Olga is working onCollaborative element… still do not know but something should be done there