Making assumption that Organism = living biological plant/animal/microbe… that is studied. Therefore “Sample type” renamed “Organism type” Also making.

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Presentation transcript:

Making assumption that Organism = living biological plant/animal/microbe… that is studied. Therefore “Sample type” renamed “Organism type” Also making assumption that Sample = part (or whole) of an organism that is dissected/preserved for metabolomics analysis. Slide 2 – suggested new grouping of fields Slides 3-5 – case studies Slide 6 – order of entry into database that would help to clarify what was done where.

Description of field SITE See 4.2 in doc Description of lab “SITE” (hopefully covered by in vivo/ mammalian but think we need to do independently) TREATMENT of (live) organism See 4.3 in doc (last 6 entries) ORGANISM type See 4.3 in doc (first 12 entries) TREATMENT of (dead) sample See 4.3 in doc (last 6 entries) Core parameters, (not experimental design/treatments) See in doc Terrestrial specific parameters See in doc Aquatic specific parameters See in doc Airborne specific parameters High level experimental design Field study? Field to lab study? Lab to field study? Lab study? Other? Dissection/ preservation parameters e.g. freeze liquid nitrogen Transportation parameters e.g. submerged in bucket in seawater Core parameters (see 4.3 in doc) Terrestrial specific parameters Aquatic specific parameters e.g. freshwater aquarium Airborne specific parameters “Transportation” parameters e.g. frozen on dry ice Collection parameters e.g. netting Acclimation and husbandry parameters e.g. feeding protocol Where does organism come from? FIELD (various categories; link to below) or LAB RAISED (various categories; link to below) or COMMERCIAL SUPPLIER? Core parameters, (not experimental design/treatments) Sample storage parameters e.g. -80 Core parameters, inc. experimental design/treatments Including…… Exposure parameters e.g. toxins, where?

Description of field SITE See 4.2 in doc Description of lab “SITE” (hopefully covered by in vivo/ mammalian but think we need to do independently) TREATMENT of (live) organism See 4.3 in doc (last 6 entries) ORGANISM type See 4.3 in doc (first 12 entries) TREATMENT of (dead) sample See 4.3 in doc (last 6 entries) Core parameters, (not experimental design/treatments) See in doc Aquatic specific parameters See in doc Airborne specific parameters High level experimental design Field study? Field to lab study? Lab to field study? Lab study? Other? Dissection/ preservation parameters e.g. freeze liquid nitrogen Transportation parameters e.g. submerged in bucket in seawater Core parameters (see 4.3 in doc) Terrestrial specific parameters Aquatic specific parameters e.g. freshwater aquarium Airborne specific parameters “Transportation” parameters e.g. frozen on dry ice Collection parameters e.g. netting Acclimation and husbandry parameters e.g. feeding protocol Where does organism come from? FIELD (various categories; link to below) or LAB RAISED (various categories; link to below) or COMMERCIAL SUPPLIER? Core parameters, (not experimental design/treatments) Sample storage parameters e.g. -80 Core parameters, inc. experimental design/treatments Including…… Exposure parameters e.g. toxins, where? e.g. fish collected and preserved from a river 4 Terrestrial specific parameters See in doc

Description of field SITE See 4.2 in doc Description of lab “SITE” (hopefully covered by in vivo/ mammalian but think we need to do independently) TREATMENT of (live) organism See 4.3 in doc (last 6 entries) ORGANISM type See 4.3 in doc (first 12 entries) TREATMENT of (dead) sample See 4.3 in doc (last 6 entries) Core parameters, (not experimental design/treatments) See in doc Aquatic specific parameters See in doc Airborne specific parameters High level experimental design Field study? Field to lab study? Lab to field study? Lab study? Other? Dissection/ preservation parameters e.g. freeze liquid nitrogen Transportation parameters e.g. submerged in bucket in seawater Core parameters (see 4.3 in doc) Terrestrial specific parameters Aquatic specific parameters e.g. freshwater aquarium Airborne specific parameters “Transportation” parameters e.g. frozen on dry ice Collection parameters e.g. netting Acclimation and husbandry parameters e.g. feeding protocol Where does organism come from? FIELD (various categories; link to below) or LAB RAISED (various categories; link to below) or COMMERCIAL SUPPLIER? Core parameters, (not experimental design/treatments) Sample storage parameters e.g. -80 Core parameters, inc. experimental design/treatments Including…… Exposure parameters e.g. toxins, where? e.g. earthworm collected from field, returned to lab for toxicity studies, and then preserved 4 6 Terrestrial specific parameters See in doc 5

Description of field SITE See 4.2 in doc Description of lab “SITE” (hopefully covered by in vivo/ mammalian but think we need to do independently) TREATMENT of (live) organism See 4.3 in doc (last 6 entries) ORGANISM type See 4.3 in doc (first 12 entries) TREATMENT of (dead) sample See 4.3 in doc (last 6 entries) Core parameters, (not experimental design/treatments) See in doc Aquatic specific parameters See in doc Airborne specific parameters High level experimental design Field study? Field to lab study? Lab to field study? Lab study? Other? Dissection/ preservation parameters e.g. freeze liquid nitrogen Transportation parameters e.g. submerged in bucket in seawater Core parameters (see 4.3 in doc) Terrestrial specific parameters Aquatic specific parameters e.g. freshwater aquarium Airborne specific parameters “Transportation” parameters e.g. frozen on dry ice Collection parameters e.g. netting Acclimation and husbandry parameters e.g. feeding protocol Where does organism come from? FIELD (various categories; link to below) or LAB RAISED (various categories; link to below) or COMMERCIAL SUPPLIER? Core parameters, (not experimental design/treatments) Sample storage parameters e.g. -80 Core parameters, inc. experimental design/treatments Including…… Exposure parameters e.g. toxins, where? e.g. fish hatched and raised in lab, moved to cage in field, exposed to sewage, and then preserved Terrestrial specific parameters See in doc

Description of field SITE Description of lab “SITE” TREATMENT of (live) organism ORGANISM type TREATMENT of (dead) sample High level experimental design Field study? Field to lab study? Lab to field study? Lab study? Other? Define One Zero (or more) Define Zero (or more) 4 Define For each treatment field, provide link to SITE. E.g. in complex lab to field to lab experiment, would define 2 lab environments and 1 field environment, and then for each step of experimental treatment link to 1, 2 or 3. Define For each treatment field, provide link to SITE. E.g. in complex lab to field to lab experiment, would define 2 lab environments and 1 field environment, and then for each step of experimental treatment link to 1, 2 or 3.