PPI finder: a mining tool for human protein-protein interactions.
BACKGROUND: The exponential increase of published biomedical literature prompts the use of text mining tools to manage the information overload automatically. One of the most common applications is to mine protein-protein interactions (PPIs) from PubMed abstracts. Currently, most tools in mining PPI...
| Main Authors: | , , |
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| Format: | Article |
| Language: | English |
| Published: |
Public Library of Science (PLoS)
2009-01-01
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| Series: | PLoS ONE |
| Online Access: | http://europepmc.org/articles/PMC2641004?pdf=render |
| _version_ | 1818467962858766336 |
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| author | Min He Yi Wang Wei Li |
| author_facet | Min He Yi Wang Wei Li |
| author_sort | Min He |
| collection | DOAJ |
| description | BACKGROUND: The exponential increase of published biomedical literature prompts the use of text mining tools to manage the information overload automatically. One of the most common applications is to mine protein-protein interactions (PPIs) from PubMed abstracts. Currently, most tools in mining PPIs from literature are using co-occurrence-based approaches or rule-based approaches. Hybrid methods (frame-based approaches) by combining these two methods may have better performance in predicting PPIs. However, the predicted PPIs from these methods are rarely evaluated by known PPI databases and co-occurred terms in Gene Ontology (GO) database. METHODOLOGY/PRINCIPAL FINDINGS: We here developed a web-based tool, PPI Finder, to mine human PPIs from PubMed abstracts based on their co-occurrences and interaction words, followed by evidences in human PPI databases and shared terms in GO database. Only 28% of the co-occurred pairs in PubMed abstracts appeared in any of the commonly used human PPI databases (HPRD, BioGRID and BIND). On the other hand, of the known PPIs in HPRD, 69% showed co-occurrences in the literature, and 65% shared GO terms. CONCLUSIONS: PPI Finder provides a useful tool for biologists to uncover potential novel PPIs. It is freely accessible at http://liweilab.genetics.ac.cn/tm/. |
| first_indexed | 2024-04-13T21:07:24Z |
| format | Article |
| id | doaj.art-373b22bfd1fd4aebadf57cb52f68ac69 |
| institution | Directory Open Access Journal |
| issn | 1932-6203 |
| language | English |
| last_indexed | 2024-04-13T21:07:24Z |
| publishDate | 2009-01-01 |
| publisher | Public Library of Science (PLoS) |
| record_format | Article |
| series | PLoS ONE |
| spelling | doaj.art-373b22bfd1fd4aebadf57cb52f68ac692022-12-22T02:29:55ZengPublic Library of Science (PLoS)PLoS ONE1932-62032009-01-0142e455410.1371/journal.pone.0004554PPI finder: a mining tool for human protein-protein interactions.Min HeYi WangWei LiBACKGROUND: The exponential increase of published biomedical literature prompts the use of text mining tools to manage the information overload automatically. One of the most common applications is to mine protein-protein interactions (PPIs) from PubMed abstracts. Currently, most tools in mining PPIs from literature are using co-occurrence-based approaches or rule-based approaches. Hybrid methods (frame-based approaches) by combining these two methods may have better performance in predicting PPIs. However, the predicted PPIs from these methods are rarely evaluated by known PPI databases and co-occurred terms in Gene Ontology (GO) database. METHODOLOGY/PRINCIPAL FINDINGS: We here developed a web-based tool, PPI Finder, to mine human PPIs from PubMed abstracts based on their co-occurrences and interaction words, followed by evidences in human PPI databases and shared terms in GO database. Only 28% of the co-occurred pairs in PubMed abstracts appeared in any of the commonly used human PPI databases (HPRD, BioGRID and BIND). On the other hand, of the known PPIs in HPRD, 69% showed co-occurrences in the literature, and 65% shared GO terms. CONCLUSIONS: PPI Finder provides a useful tool for biologists to uncover potential novel PPIs. It is freely accessible at http://liweilab.genetics.ac.cn/tm/.http://europepmc.org/articles/PMC2641004?pdf=render |
| spellingShingle | Min He Yi Wang Wei Li PPI finder: a mining tool for human protein-protein interactions. PLoS ONE |
| title | PPI finder: a mining tool for human protein-protein interactions. |
| title_full | PPI finder: a mining tool for human protein-protein interactions. |
| title_fullStr | PPI finder: a mining tool for human protein-protein interactions. |
| title_full_unstemmed | PPI finder: a mining tool for human protein-protein interactions. |
| title_short | PPI finder: a mining tool for human protein-protein interactions. |
| title_sort | ppi finder a mining tool for human protein protein interactions |
| url | http://europepmc.org/articles/PMC2641004?pdf=render |
| work_keys_str_mv | AT minhe ppifinderaminingtoolforhumanproteinproteininteractions AT yiwang ppifinderaminingtoolforhumanproteinproteininteractions AT weili ppifinderaminingtoolforhumanproteinproteininteractions |