Humans and machines in biomedical knowledge curation: hypertrophic cardiomyopathy molecular mechanisms’ representation
Abstract Background Biomedical knowledge is dispersed in scientific literature and is growing constantly. Curation is the extraction of knowledge from unstructured data into a computable form and could be done manually or automatically. Hypertrophic cardiomyopathy (HCM) is the most common inherited...
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| Format: | Article |
| Language: | English |
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BMC
2021-10-01
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| Series: | BioData Mining |
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| Online Access: | https://doi.org/10.1186/s13040-021-00279-2 |
| _version_ | 1831679082102784000 |
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| author | Mila Glavaški Lazar Velicki |
| author_facet | Mila Glavaški Lazar Velicki |
| author_sort | Mila Glavaški |
| collection | DOAJ |
| description | Abstract Background Biomedical knowledge is dispersed in scientific literature and is growing constantly. Curation is the extraction of knowledge from unstructured data into a computable form and could be done manually or automatically. Hypertrophic cardiomyopathy (HCM) is the most common inherited cardiac disease, with genotype–phenotype associations still incompletely understood. We compared human- and machine-curated HCM molecular mechanisms’ models and examined the performance of different machine approaches for that task. Results We created six models representing HCM molecular mechanisms using different approaches and made them publicly available, analyzed them as networks, and tried to explain the models’ differences by the analysis of factors that affect the quality of machine-curated models (query constraints and reading systems’ performance). A result of this work is also the Interactive HCM map, the only publicly available knowledge resource dedicated to HCM. Sizes and topological parameters of the networks differed notably, and a low consensus was found in terms of centrality measures between networks. Consensus about the most important nodes was achieved only with respect to one element (calcium). Models with a reduced level of noise were generated and cooperatively working elements were detected. REACH and TRIPS reading systems showed much higher accuracy than Sparser, but at the cost of extraction performance. TRIPS proved to be the best single reading system for text segments about HCM, in terms of the compromise between accuracy and extraction performance. Conclusions Different approaches in curation can produce models of the same disease with diverse characteristics, and they give rise to utterly different conclusions in subsequent analysis. The final purpose of the model should direct the choice of curation techniques. Manual curation represents the gold standard for information extraction in biomedical research and is most suitable when only high-quality elements for models are required. Automated curation provides more substance, but high level of noise is expected. Different curation strategies can reduce the level of human input needed. Biomedical knowledge would benefit overwhelmingly, especially as to its rapid growth, if computers were to be able to assist in analysis on a larger scale. |
| first_indexed | 2024-12-20T05:12:11Z |
| format | Article |
| id | doaj.art-c2859dfcc83f4970b302a45e7df32ce2 |
| institution | Directory Open Access Journal |
| issn | 1756-0381 |
| language | English |
| last_indexed | 2024-12-20T05:12:11Z |
| publishDate | 2021-10-01 |
| publisher | BMC |
| record_format | Article |
| series | BioData Mining |
| spelling | doaj.art-c2859dfcc83f4970b302a45e7df32ce22022-12-21T19:52:15ZengBMCBioData Mining1756-03812021-10-0114112510.1186/s13040-021-00279-2Humans and machines in biomedical knowledge curation: hypertrophic cardiomyopathy molecular mechanisms’ representationMila Glavaški0Lazar Velicki1Faculty of Medicine, University of Novi SadFaculty of Medicine, University of Novi SadAbstract Background Biomedical knowledge is dispersed in scientific literature and is growing constantly. Curation is the extraction of knowledge from unstructured data into a computable form and could be done manually or automatically. Hypertrophic cardiomyopathy (HCM) is the most common inherited cardiac disease, with genotype–phenotype associations still incompletely understood. We compared human- and machine-curated HCM molecular mechanisms’ models and examined the performance of different machine approaches for that task. Results We created six models representing HCM molecular mechanisms using different approaches and made them publicly available, analyzed them as networks, and tried to explain the models’ differences by the analysis of factors that affect the quality of machine-curated models (query constraints and reading systems’ performance). A result of this work is also the Interactive HCM map, the only publicly available knowledge resource dedicated to HCM. Sizes and topological parameters of the networks differed notably, and a low consensus was found in terms of centrality measures between networks. Consensus about the most important nodes was achieved only with respect to one element (calcium). Models with a reduced level of noise were generated and cooperatively working elements were detected. REACH and TRIPS reading systems showed much higher accuracy than Sparser, but at the cost of extraction performance. TRIPS proved to be the best single reading system for text segments about HCM, in terms of the compromise between accuracy and extraction performance. Conclusions Different approaches in curation can produce models of the same disease with diverse characteristics, and they give rise to utterly different conclusions in subsequent analysis. The final purpose of the model should direct the choice of curation techniques. Manual curation represents the gold standard for information extraction in biomedical research and is most suitable when only high-quality elements for models are required. Automated curation provides more substance, but high level of noise is expected. Different curation strategies can reduce the level of human input needed. Biomedical knowledge would benefit overwhelmingly, especially as to its rapid growth, if computers were to be able to assist in analysis on a larger scale.https://doi.org/10.1186/s13040-021-00279-2Data miningCurationAutomated curationHypertrophic cardiomyopathySignaling pathwaysKnowledge graphs |
| spellingShingle | Mila Glavaški Lazar Velicki Humans and machines in biomedical knowledge curation: hypertrophic cardiomyopathy molecular mechanisms’ representation BioData Mining Data mining Curation Automated curation Hypertrophic cardiomyopathy Signaling pathways Knowledge graphs |
| title | Humans and machines in biomedical knowledge curation: hypertrophic cardiomyopathy molecular mechanisms’ representation |
| title_full | Humans and machines in biomedical knowledge curation: hypertrophic cardiomyopathy molecular mechanisms’ representation |
| title_fullStr | Humans and machines in biomedical knowledge curation: hypertrophic cardiomyopathy molecular mechanisms’ representation |
| title_full_unstemmed | Humans and machines in biomedical knowledge curation: hypertrophic cardiomyopathy molecular mechanisms’ representation |
| title_short | Humans and machines in biomedical knowledge curation: hypertrophic cardiomyopathy molecular mechanisms’ representation |
| title_sort | humans and machines in biomedical knowledge curation hypertrophic cardiomyopathy molecular mechanisms representation |
| topic | Data mining Curation Automated curation Hypertrophic cardiomyopathy Signaling pathways Knowledge graphs |
| url | https://doi.org/10.1186/s13040-021-00279-2 |
| work_keys_str_mv | AT milaglavaski humansandmachinesinbiomedicalknowledgecurationhypertrophiccardiomyopathymolecularmechanismsrepresentation AT lazarvelicki humansandmachinesinbiomedicalknowledgecurationhypertrophiccardiomyopathymolecularmechanismsrepresentation |