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Research data keyboard_double_arrow_right Collection 2016Publisher:Figshare Funded by:EC | BIOBANKCLOUD, FCT | LARGE-SCALE INFORMATICS S..., FCT | SFRH/BD/48035/2008 +1 projectsEC| BIOBANKCLOUD ,FCT| LARGE-SCALE INFORMATICS SYSTEMS LABORATORY ,FCT| SFRH/BD/48035/2008 ,FCT| Centre of Statistics and its ApplicationsAuthors: Bastos, Hugo; Sousa, Lisete; Clarke, Luka; Couto, Francisco;Bastos, Hugo; Sousa, Lisete; Clarke, Luka; Couto, Francisco;Abstract Background Biological sequences, such as proteins, have been provided with annotations that assign functional information. These functional annotations are associations of proteins (or other biological sequences) with descriptors characterizing their biological roles. However, not all proteins are fully (or even at all) annotated. This annotation incompleteness limits our ability to make sound assertions about the functional coherence within sets of proteins. Annotation incompleteness is a problematic issue when measuring semantic functional similarity of biological sequences since they can only capture a limited amount of all the semantic aspects the sequences may encompass. Methods Instead of relying uniquely on single (reductive) metrics, this work proposes a comprehensive approach for assessing functional coherence within protein sets. The approach entails using visualization and term enrichment techniques anchored in specific domain knowledge, such as a protein family. For that purpose we evaluate two novel functional coherence metrics, mUI and mGIC that combine aspects of semantic similarity measures and term enrichment. Results These metrics were used to effectively capture and measure the local similarity cores within protein sets. Hence, these metrics coupled with visualization tools allow an improved grasp on three important functional annotation aspects: completeness, agreement and coherence. Conclusions Measuring the functional similarity between proteins based on their annotations is a non trivial task. Several metrics exist but due both to characteristics intrinsic to the nature of graphs and extrinsic natures related to the process of annotation each measure can only capture certain functional annotation aspects of proteins. Hence, when trying to measure the functional coherence of a set of proteins a single metric is too reductive. Therefore, it is valuable to be aware of how each employed similarity metric works and what similarity aspects it can best capture. Here we test the behaviour and resilience of some similarity metrics.
add ClaimPlease grant OpenAIRE to access and update your ORCID works.This Research product is the result of merged Research products in OpenAIRE.
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You have already added works in your ORCID record related to the merged Research product.All Research productsarrow_drop_down <script type="text/javascript"> <!-- document.write('<div id="oa_widget"></div>'); document.write('<script type="text/javascript" src="https://www.openaire.eu/index.php?option=com_openaire&view=widget&format=raw&projectId=10.6084/m9.figshare.c.3644354.v1&type=result"></script>'); --> </script>
For further information contact us at helpdesk@openaire.eu0 citations 0 popularity Average influence Average impulse Average Powered by BIP!more_vert add ClaimPlease grant OpenAIRE to access and update your ORCID works.This Research product is the result of merged Research products in OpenAIRE.
You have already added works in your ORCID record related to the merged Research product.This Research product is the result of merged Research products in OpenAIRE.
You have already added works in your ORCID record related to the merged Research product.All Research productsarrow_drop_down <script type="text/javascript"> <!-- document.write('<div id="oa_widget"></div>'); document.write('<script type="text/javascript" src="https://www.openaire.eu/index.php?option=com_openaire&view=widget&format=raw&projectId=10.6084/m9.figshare.c.3644354.v1&type=result"></script>'); --> </script>
For further information contact us at helpdesk@openaire.euResearch data keyboard_double_arrow_right Dataset 2016Publisher:Figshare Funded by:EC | BIOBANKCLOUD, FCT | LARGE-SCALE INFORMATICS S..., FCT | SFRH/BD/48035/2008 +1 projectsEC| BIOBANKCLOUD ,FCT| LARGE-SCALE INFORMATICS SYSTEMS LABORATORY ,FCT| SFRH/BD/48035/2008 ,FCT| Centre of Statistics and its ApplicationsAuthors: Bastos, Hugo; Sousa, Lisete; Clarke, Luka; Couto, Francisco;Bastos, Hugo; Sousa, Lisete; Clarke, Luka; Couto, Francisco;Average similarity as measured by six different metrics for each of the discrete levels of noise. (XLS 50 kb)
add ClaimPlease grant OpenAIRE to access and update your ORCID works.This Research product is the result of merged Research products in OpenAIRE.
You have already added works in your ORCID record related to the merged Research product.This Research product is the result of merged Research products in OpenAIRE.
You have already added works in your ORCID record related to the merged Research product.All Research productsarrow_drop_down <script type="text/javascript"> <!-- document.write('<div id="oa_widget"></div>'); document.write('<script type="text/javascript" src="https://www.openaire.eu/index.php?option=com_openaire&view=widget&format=raw&projectId=10.6084/m9.figshare.c.3644354_d1&type=result"></script>'); --> </script>
For further information contact us at helpdesk@openaire.eu0 citations 0 popularity Average influence Average impulse Average Powered by BIP!more_vert add ClaimPlease grant OpenAIRE to access and update your ORCID works.This Research product is the result of merged Research products in OpenAIRE.
You have already added works in your ORCID record related to the merged Research product.This Research product is the result of merged Research products in OpenAIRE.
You have already added works in your ORCID record related to the merged Research product.All Research productsarrow_drop_down <script type="text/javascript"> <!-- document.write('<div id="oa_widget"></div>'); document.write('<script type="text/javascript" src="https://www.openaire.eu/index.php?option=com_openaire&view=widget&format=raw&projectId=10.6084/m9.figshare.c.3644354_d1&type=result"></script>'); --> </script>
For further information contact us at helpdesk@openaire.eu
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Research data keyboard_double_arrow_right Collection 2016Publisher:Figshare Funded by:EC | BIOBANKCLOUD, FCT | LARGE-SCALE INFORMATICS S..., FCT | SFRH/BD/48035/2008 +1 projectsEC| BIOBANKCLOUD ,FCT| LARGE-SCALE INFORMATICS SYSTEMS LABORATORY ,FCT| SFRH/BD/48035/2008 ,FCT| Centre of Statistics and its ApplicationsAuthors: Bastos, Hugo; Sousa, Lisete; Clarke, Luka; Couto, Francisco;Bastos, Hugo; Sousa, Lisete; Clarke, Luka; Couto, Francisco;Abstract Background Biological sequences, such as proteins, have been provided with annotations that assign functional information. These functional annotations are associations of proteins (or other biological sequences) with descriptors characterizing their biological roles. However, not all proteins are fully (or even at all) annotated. This annotation incompleteness limits our ability to make sound assertions about the functional coherence within sets of proteins. Annotation incompleteness is a problematic issue when measuring semantic functional similarity of biological sequences since they can only capture a limited amount of all the semantic aspects the sequences may encompass. Methods Instead of relying uniquely on single (reductive) metrics, this work proposes a comprehensive approach for assessing functional coherence within protein sets. The approach entails using visualization and term enrichment techniques anchored in specific domain knowledge, such as a protein family. For that purpose we evaluate two novel functional coherence metrics, mUI and mGIC that combine aspects of semantic similarity measures and term enrichment. Results These metrics were used to effectively capture and measure the local similarity cores within protein sets. Hence, these metrics coupled with visualization tools allow an improved grasp on three important functional annotation aspects: completeness, agreement and coherence. Conclusions Measuring the functional similarity between proteins based on their annotations is a non trivial task. Several metrics exist but due both to characteristics intrinsic to the nature of graphs and extrinsic natures related to the process of annotation each measure can only capture certain functional annotation aspects of proteins. Hence, when trying to measure the functional coherence of a set of proteins a single metric is too reductive. Therefore, it is valuable to be aware of how each employed similarity metric works and what similarity aspects it can best capture. Here we test the behaviour and resilience of some similarity metrics.
add ClaimPlease grant OpenAIRE to access and update your ORCID works.This Research product is the result of merged Research products in OpenAIRE.
You have already added works in your ORCID record related to the merged Research product.This Research product is the result of merged Research products in OpenAIRE.
You have already added works in your ORCID record related to the merged Research product.All Research productsarrow_drop_down <script type="text/javascript"> <!-- document.write('<div id="oa_widget"></div>'); document.write('<script type="text/javascript" src="https://www.openaire.eu/index.php?option=com_openaire&view=widget&format=raw&projectId=10.6084/m9.figshare.c.3644354.v1&type=result"></script>'); --> </script>
For further information contact us at helpdesk@openaire.eu0 citations 0 popularity Average influence Average impulse Average Powered by BIP!more_vert add ClaimPlease grant OpenAIRE to access and update your ORCID works.This Research product is the result of merged Research products in OpenAIRE.
You have already added works in your ORCID record related to the merged Research product.This Research product is the result of merged Research products in OpenAIRE.
You have already added works in your ORCID record related to the merged Research product.All Research productsarrow_drop_down <script type="text/javascript"> <!-- document.write('<div id="oa_widget"></div>'); document.write('<script type="text/javascript" src="https://www.openaire.eu/index.php?option=com_openaire&view=widget&format=raw&projectId=10.6084/m9.figshare.c.3644354.v1&type=result"></script>'); --> </script>
For further information contact us at helpdesk@openaire.euResearch data keyboard_double_arrow_right Dataset 2016Publisher:Figshare Funded by:EC | BIOBANKCLOUD, FCT | LARGE-SCALE INFORMATICS S..., FCT | SFRH/BD/48035/2008 +1 projectsEC| BIOBANKCLOUD ,FCT| LARGE-SCALE INFORMATICS SYSTEMS LABORATORY ,FCT| SFRH/BD/48035/2008 ,FCT| Centre of Statistics and its ApplicationsAuthors: Bastos, Hugo; Sousa, Lisete; Clarke, Luka; Couto, Francisco;Bastos, Hugo; Sousa, Lisete; Clarke, Luka; Couto, Francisco;Average similarity as measured by six different metrics for each of the discrete levels of noise. (XLS 50 kb)
add ClaimPlease grant OpenAIRE to access and update your ORCID works.This Research product is the result of merged Research products in OpenAIRE.
You have already added works in your ORCID record related to the merged Research product.This Research product is the result of merged Research products in OpenAIRE.
You have already added works in your ORCID record related to the merged Research product.All Research productsarrow_drop_down <script type="text/javascript"> <!-- document.write('<div id="oa_widget"></div>'); document.write('<script type="text/javascript" src="https://www.openaire.eu/index.php?option=com_openaire&view=widget&format=raw&projectId=10.6084/m9.figshare.c.3644354_d1&type=result"></script>'); --> </script>
For further information contact us at helpdesk@openaire.eu0 citations 0 popularity Average influence Average impulse Average Powered by BIP!more_vert add ClaimPlease grant OpenAIRE to access and update your ORCID works.This Research product is the result of merged Research products in OpenAIRE.
You have already added works in your ORCID record related to the merged Research product.This Research product is the result of merged Research products in OpenAIRE.
You have already added works in your ORCID record related to the merged Research product.All Research productsarrow_drop_down <script type="text/javascript"> <!-- document.write('<div id="oa_widget"></div>'); document.write('<script type="text/javascript" src="https://www.openaire.eu/index.php?option=com_openaire&view=widget&format=raw&projectId=10.6084/m9.figshare.c.3644354_d1&type=result"></script>'); --> </script>
For further information contact us at helpdesk@openaire.eu