Are you an MSc holder in Bioinformatics interested to learn more on similarity metrics, microbiome (meta)data, climate change, and/or text mining?
A position is now available in CCMRI!
Find out more here (job post in Greek, DOATAP requirement applies)
Climate Change Metagenomic Record Index (CCMRI): a dynamic researcher-notification and sample classification system
Climate Change (CC) is reshaping all ecosystem processes and structures. Its research has traditionally focused on abiotic factors. Microorganisms, major participants of biogeochemical cycles, both affect and are affected by CC. Thus, their analysis is important too. Metagenomic studies can describe a sample’s microbial community composition and sum its biochemical potential. Global resources offer access to public metagenomic records. However, given the environmental genomics data deluge, locating the CC-related ones is a tedious process.
CCMRI aims to harvest the metagenomic records pertaining to CC and offer researchers with a web-based notification service when relevant records become available.
Web retrieval and text-mining will be combined to detect CC evidence in the metadata and the literature of metagenomic records. Pertinent text will be scanned for mentions of CC descriptive keywords. Previous team experience on Named Entity Recognition will be employed to outperform conventional keyword based searches.
A high-level set of metagenomic record Classes-of-Interest (CoIs) will be defined reflecting broad topics of CC relatedness (e.g. biogeochemical processes or types of anthropogenic impact). CoIs will help both user navigation and also serve as a hypothesis generation mechanism basis. Taxonomic and functional profiles for each CoI will be computed. CCMRI will allow users to match their samples against those of each CoI. Significant similarities can then offer clues as to a sample’s source or other phenomena occurring within.
Collaboration with molecular ecologists will drive easy and user-friendly web software development. Also, IMBBC samples will be analysed. Sample proximity to fresh or to marine water inputs and links to nearby agri-, aqua-culture activities, will be explored.
CCMRI closes the gap between climate change research and microbial ecology. Its News Tracker and Sample Matcher applications can be of immediate use to microbiologists, ecologists, climatologists. Epidemiologists, environmental/health organisations and policymakers can benefit too by timely notifications.
Correspondence: pafilis[at]hcmr.gr; ccmri[at]hcmr.gr; Tel: +30 2810 337748
Institute of Marine Biology, Biotechnology & Aquaculture HCMR Thalassocosmos 71500 Gournes, Crete, Greece P.O.Box 2214, 71003 Heraklion, Crete, Greece
Funded from the Hellenic Foundation for Research and Innovation (HFRI) (grant No 2772).