• Share
  • Email
  • Embed
  • Like
  • Save
  • Private Content

Loading…

Flash Player 9 (or above) is needed to view presentations.
We have detected that you do not have it on your computer. To install it, go here.

Like this presentation? Why not share!

A proposed model of knowledge representation and the coding of knowledge embedded in texts of Web published scientific articles

on

  • 2,450 views

Carlos Henrique Marcondes, Marília Alvarenga Rocha Mendonça, Luciana Reis Malheiros ...

Carlos Henrique Marcondes, Marília Alvarenga Rocha Mendonça, Luciana Reis Malheiros
Department of Information Science
Department of Physiology and Pharmacology
Federal Fluminense University, R. Lara Vilela, 126, 24210-590, Niterói, RJ, Brazil

Statistics

Views

Total Views
2,450
Views on SlideShare
2,446
Embed Views
4

Actions

Likes
2
Downloads
0
Comments
0

1 Embed 4

http://www.slideshare.net 4

Accessibility

Categories

Upload Details

Uploaded via as Adobe PDF

Usage Rights

© All Rights Reserved

Report content

Flagged as inappropriate Flag as inappropriate
Flag as inappropriate

Select your reason for flagging this presentation as inappropriate.

Cancel
  • Full Name Full Name Comment goes here.
    Are you sure you want to
    Your message goes here
    Processing…
Post Comment
Edit your comment

    A proposed model of knowledge representation and the coding of knowledge embedded in texts of Web published scientific articles A proposed model of knowledge representation and the coding of knowledge embedded in texts of Web published scientific articles Presentation Transcript

    • A proposed model of knowledge representation and coding of knowledge embedded in texts of Web published scientific articles – code 125 InsciT2006 Conference, Mérida, Spain, Out. 2006 Carlos Henrique Marcondes, marcon@vm.uff.br, Marília Alvarenga Rocha Mendonça, Department of Information Science Luciana Reis Malheiros Department of Physiology and Pharmacology Federal Fluminense University, Brazil Keywords: electronic publishing, scientific methodology, scientific knowledge, scientific communication, knowledge representation, ontologies – 22 slides
    • Context “Information overload” Semantic Web Initiative Scholar electronic journals are still based on print model and do not take full advantage of facilities offered by the Web environment Web Ontologies are becoming the humanity public knowledge bases, alternative to collections in libraries
    • Problem Knowledge is embedded in the text of scientific articles for human reading, in an unstructured format, not adequate for program processing Scientific communication is a slow social process which depends on discourse, text producing and reading/interpreting/inquiring until new knowledge is incorporated to the corpus of Science The potential of new IT has been applied to modern bibliographic information systems to improve scientific communication, providing fast notification and access to full-text scientific documents. But IT is not yet used to directly process the knowledge embedded in the text of scientific articles
    • Questions Is it feasible the development of an authoring/self- publishing tool which enables the Web publishing of scientific articles both as text and in program readable format, adequate for software agents processing? Knowledge thus extracted, marked-up and recorded in program readable format, will enable inferences by software agents: consistency checking and validation of new contributions to Science, scientific discovery identification, rich semantic retrieval, etc
    • Research objetives To explore the potential of scientific journals Web published as cognitive tools in the Semantic Web context Propose and validate a model to the knowledge structure embedded in the text of scientific articles in program readable format To use the this model to identify novelties in Science To establish functional requirements and specification for the development of an authoring/self-publishing tool which enables the extraction and mark-up of knowledge as a by- product of writing-publishing a scientific an article by a scholar
    • Hypothesis Scientific articles are highly structured pieces of texts reflecting reasoning procedures established by the Scientific Method “The text of observational and experimental articles is usually… divided into sections with the headings IMRAD - Introduction, Methods, Results, and Discussion. This structure is not simply an arbitrary publication format, but rather a direct reflection of the process of scientific discovery”, Uniform Requirements for Manuscripts Submitted to Biomedical Journals (http://www.icmje.org) Knowledge embedded in the text of scientific articles has the form of relations between phenomena as, for ex: “to smoke causes lung carcinoma” A hypothesi (from Greek ὑπόθεσις) is a suggested explanation of a phenomenon or reasoned proposal suggesting a possible correlation between multiple phenomena, WikiPedia,http://en.wikipedia.org/wiki/Hypothesis “knowledge is a structure of concepts linked by their relations and information is a small part of such a structure” (BROOKES, 1980, p. 131)
    • Knowledge as Relations Knowledge as relations between phenomena appear in different elements of Scientific Method In PROBLEM, as a question In HYPOTHESIS as a possible explanation In CONCLUSION as a statement
    • Methodology An initial model was proposed, based on elements of scientific method, as Problem, Hypotheses, Methodology, Results and Conclusion Model was tested with 50 journal articles 20 from Memorias do Instituto Oswaldo Cruz, http://www.scielo.br/revistas/mioc 20 from Brazilian Journal of Medical and Biological Research, http://www.scielo.br/revistas/bjmbr 9 about Stem cells in international journals (in course) Test results were used to enhance the Model
    • The Proposed Model Model of Authoring/Self-publishing Web environment Model of Reasoning Procedures in scientific articles Model of Knowledge Representation of knowledge embedded in scientific articles texts, as a task ontology, identifying elements of scientific reasoning as Data, Problem, Hypotheses, Material/Method, Results and Conclusion and marking-up/recording it in program readable format
    • Authoring/Self-Publishing Web environment A IMPOR Eas kjjsd dj sdk skdkl Author/ A IMPOR skls a fd g Eas kjjsdggfgg g gfg dj scholar sdk skdkl skls a fd g gfg ggfgg g Authoring tool Scientific literature in a domain, Web published Semantic A IMPOR citaions Eas kjjsd dj sdk skdkl skls a fd g gfg ggfgg g Semantic Scientific Knowledge relations article - text represented in Web ontology (like program UMLS) readable format Semantic retrieval, validate and consistent checking tools Researcher, reader
    • Reasoning Procedures in scientific articles Experimental-inductive articles Experimental-deductive articles Theoretical-abductive articles
    • Reasoning Procedures in scientific articles Experimental-inductive articles a PROBLEM is identified, with the following aspects and data; a possible solution to this PROBLEM can be based on the following new HYPOTHESIS; on the basis of this original HYPOTHESIS the PROBLEM has the following empirical MANIFSTATION; we developed an experiment to test this MANIFESTATION and it comes at the following RESULTS.
    • Reasoning Procedures in scientific articles Experimental-deductive articles a PROBLEM is identified, with the following aspects and data; in literature the previous authors/HYPOTHESIS are proposed; we choose the following previous HYPOTHESIS which has this empirical MANIFESTATION; we test, enlarge and re-contextualize this HYPOTHESIS; the test shows the following RESULTS in this new CONTEXT.
    • Reasoning Procedures in scientific articles Theoretic-abdutive articles a PROBLEM is identified, with the following aspects and data; the previous authors/HYPOTHESIS are not satisfactory to solve the PROBLEM due to the following criticism; so, we propose this original HYPOTHESIS which we consider as a new pathway to solve the PROBLEM.
    • Analysis procedure (simulating the authoring/Self-Publishing tool) CAMARA, Geni NL, CERQUEIRA, Daniela M, OLIVEIRA, Ana PG et al. Prevalence of human papillomavirus types in women with pre-neoplastic and neoplastic cervical lesions in the Federal District of Brazil. Mem. Inst. Oswaldo Cruz. [online]. Oct. 2003, vol.98, no.7 3 steps: Type of reasoning is identified: experimental-deductive “Records of knowledge” are identified in the text as the main hypothesis stated by the author: Antecedent: HPV Type of Relation: causes Consequent: pre-neoplastic and neoplastic cervical lesions Each of these elements are mapped to “Public Knowledge” - UMLS, UMLS Semantic Network* Papillomavirus, Human “Causes” , UMLS Semantic network relation R147 Colonic Neoplasms, Tumor Vírus Infections /pathology, Tumor Vírus Infections /virology *We used DECS, portuguese version of MESH – Medical Subject Headings -, the main Vocabulary in UMLS
    • Model of knowledge representation – Ontology for knowledge in scientific articles
    • Model potentialities – semantic retrieval which other articles have hypothesis suggesting HPV as the cervical neoplasias cause in women? which articles have hypothesis suggesting causes other then HPV to cervical neoplasias in women? which articles have hypothesis suggesting HPV as cervical neoplasias cause in groups different from women? which articles have hypothesis suggesting HPV as the cause of other pathologies different from neoplasias? which articles have hypothesis suggesting HPV as cervical neoplasias cause in different contexts? (not in women from Federal District, Brazil).
    • Model potentialities Software agents can navigate throughout a network of scientific articles published according to the model outlined and make inferences … To identify novelties in Science A failure to map one or more elements of a “record of knowledge” may be an trace of a scientific discovery To validate and consistency check of new contributions to Science Is the knowledge in an article consistent with knowledge recorded in a public Web ontology?
    • Results EXP- EXP- THEO- JOURNALS TOTAL INDUCTIVE DEDUCTIVE ABDUCTIVE MIOC 4 15 1 20 BJMBR 4 14 2 20 STEM- 7 2 0 9 CELLS TOTAL 15 31 3 49
    • Results Mapping elements of relation found in articles is a fundamental step of the model proposed: we compared concepts found with MESH indexing provided by the article Medline record many times it was not possible to map concepts found; due to their specificity they were not found in UMLS many relationships in articles were not found in UMSL Semantic Network too Theoretic-abductive articles do not fit into the IMRAD structure; not always they fit into the reasoning procedures proposed; some reviews articles could be classified as theoretic-abdutive articles
    • Open questions and future research Is the model proposed feasible in scientific areas others than Health Science? The need of a taxonomy of relations in Science Is it feasible a Sm-ML – Scientific Methodology Markup Language? Guidelines for the development of a Scientific editor to implement the proposed model
    • Comments are welcome! http://www.professores.uff.br/marcondes marcon@vm.uff.br