PMC:4331675 / 5687-7705 JSONTXT

{"project":"2_test","denotations":[{"id":"25708840-18823568-14883597","span":{"begin":118,"end":120},"obj":"18823568"},{"id":"25708840-22115179-14883598","span":{"begin":121,"end":123},"obj":"22115179"},{"id":"25708840-23161681-14883599","span":{"begin":722,"end":724},"obj":"23161681"},{"id":"25708840-19850723-14883600","span":{"begin":1078,"end":1080},"obj":"19850723"},{"id":"25708840-22096227-14883601","span":{"begin":1089,"end":1091},"obj":"22096227"},{"id":"25708840-23203989-14883602","span":{"begin":1103,"end":1105},"obj":"23203989"},{"id":"25708840-14681454-14883603","span":{"begin":1113,"end":1115},"obj":"14681454"},{"id":"25708840-18988627-14883604","span":{"begin":1124,"end":1126},"obj":"18988627"},{"id":"25708840-16381906-14883605","span":{"begin":1144,"end":1146},"obj":"16381906"}],"text":"Data collection and integration\nThere are several protein interaction databases, such as PINA, STRING, and iRefIndex [13,14], which allow downloading PPI information for academic purposes free of charge, but such downloaded files from different databases do not take on a common format. In this cisPath package, functions are provided to format the downloaded files from the PINA, STRING and iRefIndex databases into a standard workable format. To remove redundant interactions, UniProt Knowledgebase (UniProtKB) accession numbers are used as unique protein identifiers. UniProtKB is a part of the UniProt database and serves as a central hub for collection of functional information on proteins with accurate annotation [15]. UniProtKB consists of two sections including UniProtKB/Swiss-Prot (reviewed and manually annotated) and UniProtKB/TrEMBL (unreviewed and automatically annotated). Proteins with names that cannot be mapped to UniProtKB accession numbers are discarded.\nThe PINA database includes unified PPI data integrated from six manually curated databases: IntAct [16], MINT [17], BioGRID [18], DIP [19], HPRD [20] and MIPS MPact [21]. Like PINA, the iRefIndex database also provides an index of protein interactions integrated from primary interaction databases. PPI data downloaded from the PINA and iRefIndex databases contain the PubMed IDs of corresponding papers which support the PPIs. The STRING database contains not only known PPIs but also predicted protein associations with confidence scores. The latest version of STRING (v9.1) currently covers 5,214,234 proteins from 1,133 organisms. Although the PINA and iRefIndex databases are both integrated from manually curated databases, many distinct interactions exist in each case. Thus, several functions have been included in this package to format downloaded PPI data from different databases, consequently allowing users to edit downloaded information or merge them with privately collected data to construct more comprehensive PPI networks."}