An annotation scheme for citation function

We study the interplay of the discourse structure of a scientific argument with formal citations. One subproblem of this is to classify academic citations in scientific articles according to their rhetorical function, e.g., as a rival approach, as a part of the solution, or as a flawed approach that justifies the current research. Here, we introduce our annotation scheme with 12 categories, and present an agreement study

Annotation scheme for citation classification in scientific literature

El análisis de citas bibliográficas que usa variaciones de métodos de conteo provoca deformaciones en la evaluación del impacto. Para enriquecer el cálculo de los factores de impacto se necesita entender el tipo de influencia de los aportes de un investigador sobre el autor que los menciona. Para ello, se requiere realizar análisis de contenido del contexto de las citas que permita obtener su función, polaridad e influencia. El presente artículo trata sobre la definición de un esquema de anotación tendiente a la creación de un corpus de acceso público que sea la base de trabajo colaborativo en este campo, con miras al desarrollo de sistemas que permitan llevar adelante tareas de análisis de contenido con el objetivo planteado.Citation analysis that uses counting methods causes deformations in impact factor assessment. To enrich impact factor calculation is necessary to understand the kind of influence that the contributions of an author have over another´s work. For this purpose, it is required to perform citation content analysis to obtain its function, polarity and influence in a context within an article that mentioned it. In this paper, we focus in the definition of an annotation scheme aimed at creating a public access corpus that be the basis of collaborative work in this field, in order to develop citation content analysis to obtain criteria for impact evaluation

EFICAz²: enzyme function inference by a combined approach enhanced by machine learning

©2009 Arakaki et al; licensee BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. The electronic version of this article is the complete one and can be found online at: http://www.biomedcentral.com/1471-2105/10/107doi:10.1186/1471-2105-10-107Background: We previously developed EFICAz, an enzyme function inference approach that combines predictions from non-completely overlapping component methods. Two of the four components in the original EFICAz are based on the detection of functionally discriminating residues (FDRs). FDRs distinguish between member of an enzyme family that are homofunctional (classified under the EC number of interest) or heterofunctional (annotated with another EC number or lacking enzymatic activity). Each of the two FDR-based components is associated to one of two specific kinds of enzyme families. EFICAz exhibits high precision performance, except when the maximal test to training sequence identity (MTTSI) is lower than 30%. To improve EFICAz's performance in this regime, we: i) increased the number of predictive components and ii) took advantage of consensual information from the different components to make the final EC number assignment. Results: We have developed two new EFICAz components, analogs to the two FDR-based components, where the discrimination between homo and heterofunctional members is based on the evaluation, via Support Vector Machine models, of all the aligned positions between the query sequence and the multiple sequence alignments associated to the enzyme families. Benchmark results indicate that: i) the new SVM-based components outperform their FDR-based counterparts, and ii) both SVM-based and FDR-based components generate unique predictions. We developed classification tree models to optimally combine the results from the six EFICAz components into a final EC number prediction. The new implementation of our approach, EFICAz², exhibits a highly improved prediction precision at MTTSI < 30% compared to the original EFICAz, with only a slight decrease in prediction recall. A comparative analysis of enzyme function annotation of the human proteome by EFICAz² and KEGG shows that: i) when both sources make EC number assignments for the same protein sequence, the assignments tend to be consistent and ii) EFICAz² generates considerably more unique assignments than KEGG. Conclusion: Performance benchmarks and the comparison with KEGG demonstrate that EFICAz² is a powerful and precise tool for enzyme function annotation, with multiple applications in genome analysis and metabolic pathway reconstruction. The EFICAz² web service is available at: http://cssb.biology.gatech.edu/skolnick/webservice/EFICAz2/index.htm

Do peers see more in a paper than its authors?

Recent years have shown a gradual shift in the content of biomedical publications that is freely accessible, from titles and abstracts to full text. This has enabled new forms of automatic text analysis and has given rise to some interesting questions: How informative is the abstract compared to the full-text? What important information in the full-text is not present in the abstract? What should a good summary contain that is not already in the abstract? Do authors and peers see an article differently? We answer these questions by comparing the information content of the abstract to that in citances-sentences containing citations to that article. We contrast the important points of an article as judged by its authors versus as seen by peers. Focusing on the area of molecular interactions, we perform manual and automatic analysis, and we find that the set of all citances to a target article not only covers most information (entities, functions, experimental methods, and other biological concepts) found in its abstract, but also contains 20% more concepts. We further present a detailed summary of the differences across information types, and we examine the effects other citations and time have on the content of citances

Going the distance for protein function prediction: a new distance metric for protein interaction networks

Due to an error introduced in the production process, the x-axes in the first panels of Figure 1 and Figure 7 are not formatted correctly. The correct Figure 1 can be viewed here: http://dx.doi.org/10.1371/annotation/343bf260-f6ff-48a2-93b2-3cc79af518a9In protein-protein interaction (PPI) networks, functional similarity is often inferred based on the function of directly interacting proteins, or more generally, some notion of interaction network proximity among proteins in a local neighborhood. Prior methods typically measure proximity as the shortest-path distance in the network, but this has only a limited ability to capture fine-grained neighborhood distinctions, because most proteins are close to each other, and there are many ties in proximity. We introduce diffusion state distance (DSD), a new metric based on a graph diffusion property, designed to capture finer-grained distinctions in proximity for transfer of functional annotation in PPI networks. We present a tool that, when input a PPI network, will output the DSD distances between every pair of proteins. We show that replacing the shortest-path metric by DSD improves the performance of classical function prediction methods across the board.MC, HZ, NMD and LJC were supported in part by National Institutes of Health (NIH) R01 grant GM080330. JP was supported in part by NIH grant R01 HD058880. This material is based upon work supported by the National Science Foundation under grant numbers CNS-0905565, CNS-1018266, CNS-1012910, and CNS-1117039, and supported by the Army Research Office under grant W911NF-11-1-0227 (to MEC). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript

Recognizing cited facts and principles in legal judgements

In common law jurisdictions, legal professionals cite facts and legal principles from precedent cases to support their arguments before the court for their intended outcome in a current case. This practice stems from the doctrine of stare decisis, where cases that have similar facts should receive similar decisions with respect to the principles. It is essential for legal professionals to identify such facts and principles in precedent cases, though this is a highly time intensive task. In this paper, we present studies that demonstrate that human annotators can achieve reasonable agreement on which sentences in legal judgements contain cited facts and principles (respectively, κ=0.65 and κ=0.95 for inter- and intra-annotator agreement). We further demonstrate that it is feasible to automatically annotate sentences containing such legal facts and principles in a supervised machine learning framework based on linguistic features, reporting per category precision and recall figures of between 0.79 and 0.89 for classifying sentences in legal judgements as cited facts, principles or neither using a Bayesian classifier, with an overall κ of 0.72 with the human-annotated gold standard