Data Preparation Protocols

The EUROSMALLMAMMALS database stores data from several partners characterized by capture and laboratory data. Raw data provided by EUROSMALLMAMMALS partners should be harmonized before including them in the database. This is the main task of data curator.

Here you can find the guidelines and the forms to consistently adapt your data sets to EUROSMALLMAMMALS database structure. By following this format data uploading will be faster and, more importantly, less error prone. In addition to data harmonizing, data curators also perform accurate quality checks to guarantee that only reliable data will be used during later analyses.

The following guidelines are grouped by tables composed of diverse records. Note that not all the records are compulsory and not all the tables should be filled. The partners can fill the tables by:

  1. directly entering the values within the records,
  2. choosing the most appropriate value within a defined categorized list,
  3. adding additional information not coded or included in the existing records in the generic "Notes".

In order to facilitate data preparation, if this is convenient for you, you can use a set of TEMPLATES (Excel spreadsheets) that can be filled with the partners' data. Before processing your data, please discuss with the data curators any uncertainties. If you have any problems you can always contact the data curators for technical support (eurosmallmammals.datacurator@fmach.it).

We encourage feedback, especially regarding data you believe would be valuable within the network! Currently, we are aligning the EUROSMALLMAMMALS database with the EUROMAMMALS format.

CONTENTS

ANIMAL

All the capture information stored in the database are related to specific individuals. The list of monitored animals with their characteristics is the first information that is processed as no data can be imported if those are not referenced to a specific animal listed in the database. The information must be structured in a single table "ANIMAL" (see, table structure in this template), filled with the following columns:

  • Identifier of the animal chip (code, mark, number and/or name)
  • Sex
    Entry code number for sex:
    • 1 - Male
    • 2 - Female
    • 3 - Unknown
  • Species Latin name

CAPTURE DATA

Within this group of data, we collect information about the proper capture events composed by 4 different tables. These tables include the information on proper animal handling "SAMPLING", collection of morphometric measures "BODY MEASURE" and biological samples "COLLECTED SAMPLES", and finally the parasitological screening "TICKS POSITION". Please include all capture data for each specific animal captured within a trapping project.

1) SAMPLING

Please, see template for the table structure. You are invited to use this template to format your data.

  • Sampling id
  • Animal id
  • Capture date the date when the animal was captured
  • Capture time the time (UTC) the animal was captured
  • Lost Chip a previously captured animal but with unidentifiable mark code
  • N animals number of animals contemporary captured in multiple trap
  • Reproductive status at capture
    Select TRUE/FALSE for each reproductive class:
    • Testes small
    • Testes large
    • Imperforate
    • Perforate
    • Pregnant
    • Lactating
    • Tits evident
  • Presence of ticks based on tick life stage and their position on the host
    Entry number of ticks for each life stage and in each body portion:
    • Larvae (left ear, right ear, head, body)
    • Nymphs (left ear, right ear, head, body)
    • Adults (left ear, right ear, head, body)
  • Fleas presence and number of fleas
  • Mites presence and number of mites
  • Mobile mites presence and number of mobile mites
  • Total ticks presence and number of total ticks
  • Mortality if an animal was found dead
    Entry TRUE/FALSE if mortality occurs and select code number for death cause:
    • 1 - In trap
    • 2 - Handling
    • 3 - Predation
  • Note any specific note of capture event
  • Capture type
    Entry code number for capture:
    • 1 - New individual
    • 2 - Recapture across primary sessions
    • 3 - Week recapture within primary sessions
  • Observer personelle name
  • Pelage fur color
    Entry code number for pelage:
    • 1 - Grey
    • 2 - Brown
    • 3 - Grey-Brown
    • 4 - Unknown
  • Predator species found in the trap or when considering owl pellets
    Entry code number for predator:
    • 1 - Mustela erminea
    • 2 - Mustela nivalis
    • 3 - Asio otus
    • 4 - Athene noctua
    • 5 - Bubo bubo
    • 6 - Strix aluco
    • 7 - Tyto alba
  • Project acronym
  • Session date begin and end (YYYY:MM:DD) and number of trapping nights
  • Status age class of the captured animal
    Entry code number for status:
    • 1 - Juvenile
    • 2 - Sub-adult
    • 3 - Adult
    • 4 - Unknown
  • Trap code/name of the trap where the animal was captured

2) BODY MEASURE

Please, see template for the table structure. You are invited to use this template to format your data.

  • Animal id
  • Mass animal in grams
  • Tara of the weighing bag in grams
  • Body measures 
    Entry morphometric values for each measure in centimeters:
    • Head-body length
    • Total length
    • Tail length
    • Head
    • Left ear
    • Testicles height
    • Testicles length
    • Hind left food
  • Note any specific note of body measures collection
  • Observer personelle name
  • Sampling id crescent number of Sampling id to connect this information to capture the event

3) COLLECTED SAMPLES

Please, see template for the table structure. You are invited to use this template to format your data.

  • Blood code of collected blood
  • Qt blood a quantity (ml) of collected serum first aliquot
  • Qt blood b quantity (ml) of collected serum second aliquot
  • Qt blood c quantity (ml) of collected serum third aliquot
  • Collected samples 
    Select TRUE/FALSE for each biological sample:
    • Red cells
    • DNA
    • Ear punch
    • Tail sample
  • Saliva code of collected saliva
  • Faeces form code of collected faeces in formalin
  • Faeces rnal code of collected faeces in RNALater nucleic acid preservation buffer
  • Faeces frozen code of collected faeces stored in freezers
  • Glicemia rate of glicemia
  • Urine code of collected urine
  • Qt urine quantity (ml) of urine
  • Qt salsol quantity of saline solution
  • Note any specific note of biological samples collection
  • Observer personelle name
  • Sampling id crescent number to connect this information to capture the event

4) TICKS POSITION

Please, see template for the table structure. You are invited to use this template to format your data.

  • Position tick position on host body (head, ear, body)
  • Larvae number of larvae involved in the group type
  • Nymph number of nymphs involved in the group type
  • Adult number of adults involved in the group type
  • LA aggregation number of total larvae aggregation
  • L distance larvae distance to the closest free nymph
  • Sampling id crescent number to connect this information to capture the event
  • Ticks groups type 
    Entry code number for ticks group:
    • 1 - NF free nymph
    • 2 - CF co-feeding between larvae and nymphs
    • 3 - LA larval aggregation

LABORATORY DATA

Within the laboratory data section, we collect information about the different kinds of laboratory analyses that are possible to perform using small mammal biological samples. In particular, these data are stored in 3 different tables, the first and second tables focusing on tick and rodent-borne pathogens detection through blood samples "BLOOD" and tissue samples "TISSUE", and finally the table including necropsy data "AUTOPSY" performed on dead animals found in traps or purposely killed. Please include all laboratory data for each specific animal performed within a trapping project.

1) BLOOD AND 2) TISSUE

Please, see template for "BLOOD" table structure and template for "TISSUE" table. You are invited to use these templates to format your data.

  • Detection of pathogens in the blood and in tissue 
    Select TRUE/FALSE for each pathogen:
    • TBE Tick-borne encephalitis
    • CPOX Cowpox
    • MHV Mouse Hepatitis virus
    • LCMV Lymphocytic Choriomeningitis virus
    • DOBV Dobrava virus
    • PUUMV Puumala virus
    • LJV Ljungan virus
    • BORRELIA s.l.
    • ANAPLASMA
    • EHRLICHIA
    • RICKETTSIA
    • WORMS
  • Collected sample id crescent number to connect this information to collected samples table

3) AUTOPSY

Please, see template for the table structure. You are invited to use this template to format your data.

  • embryo reabsorbation occurrence
  • tubuli epididymis presence of epididymis in male individuals
  • tubuli epididymis number
  • versiculae height versiculae seminales height in millimeters
  • versiculae length versiculae seminales length in millimeters
  • embryos number
  • embryos uterine height in millimeters
  • embryos uterine length in millimeters
  • embryos size height in millimeters
  • embryos size length in millimeters
  • regres male very old male
  • maculae cyaneae uterine stain presence, which means that female is in her first reproductive season after birth
  • litter1 number
  • litter2 number
  • litter3 number
  • litter sum
  • Organs and samples collection from autopsy 
    Select TRUE/FALSE for each sample:
    • foot sample
    • brain (frozen or fromaline)
    • liver (frozen or fromaline)
    • lung (frozen or fromaline)
    • heart (frozen or fromaline)
    • spleen (frozen or fromaline)
    • pancreas (frozen or fromaline)
    • kidney (frozen or fromaline)
    • gut alcool
    • interior faeces
  • Note any specific note on autopsy
  • Animal id
  • Observer personelle name

STUDY AREA AND DESIGN

Small mammals trapping studies are usually performed in precise study sites which are characterized by the deployment of several trapping plots, where fix number of traps are placed. In this sense, we structured 3 types of tables that describe the study area, defined by "SITE", "PLOT" and "TRAP". In addition, each trapping plot can have a specific experimental design, here below as "SAMPLING DESIGN" table.

1) SITE

Please, see template for the table structure. You are invited to use this template to format your data.

  • Site id
  • Site name study area name or code
  • Coordinates Site specify the coordinates (in lat/long) of the study area (also approximate, if not know with higher precision)
  • height elevation in meters

2) PLOT

Please, see template for the table structure. You are invited to use this template to format your data.

  • Plot id
  • Plot name trapping plot name or code
  • Coordinates Plot specify the coordinates (in lat/long) of the trapping plot (also approximate, if not know with higher precision)
  • height elevation in meters
  • Aspect classes of the trapping plot elevation (on average) 
    Entry number code for aspect class:
    • 1 - Flat (-1)
    • 2 - North (0°to 22.5°)
    • 3 - Northeast (22.5° to 67.5°)
    • 4 - East (67.5° to 112.5°)
    • 5 - Southeast (112.5° to 157.5°)
    • 6 - South (157.5° to 202.5°)
    • 7 - Southwest (202.5° to 247.5°)
    • 8 - West (247.5° to 292.5°)
    • 9 - Northwest (292.5° to 337.5°)
    • 10 - North (337.5° to 360°)
  • Sampling design id crescent number to identify the sampling design applied in this trapping plot
  • Site id crescent number to identify which study site includes this trapping plot
  • Slope classes of the trapping plot (on average) 
    Entry number code for slope class:
    • 1 - 0 to 10%
    • 2 - 11 to 20%
    • 3 - 21 to 30%
    • 4 - 31 to 40%
    • 5 - 41 to 50%
    • 6 - 51 to 60%
    • 7 - 61 to 70%
    • 8 - 71 to 80%
    • 9 - 81 to 90%

3) SAMPLING DESIGN

Please, see template for the table structure. You are invited to use this template to format your data.

  • Sampling design id
  • Sensors if any type of sensor was placed on animals
  • Design method used in the trapping plot  
    Entry number code for design type:
    • 1 - Snap-trapping
    • 2 - Pellet
    • 3 - Live-trapping
    • 4 - Opportunistic trapping
    • 5 - None
  • Dimension the number of trap used for each trapping plot and the distance in meters between the traps
  • Plot type the type of plot used to place the trap 
    Entry number code for plot type:
    • 1 - Classic grid
    • 2 - Cross-shaped grid
    • 3 - Transect
    • 4 - None
  • Sensor type the type of sensor used to track animal movement 
    Entry number code for sensor type:
    • 1 - GPS sensor
    • 2 - VHF sensor
    • 3 - Other
    • 4 - None
  • Tag the type of tag used to identify the animals 
    Entry number code for tag type:
    • 1 - Hair cutting
    • 2- Ear tagging
    • 3 - PIT tagging
    • 4 - Toe-nails clipping
    • 5 - None
  • Trap type the trap of trap used in the experimental design 
    Entry number code for trap type:
    • 1 - Sherman
    • 2 - Longworth
    • 3 - Ugglan
    • 4 - Wooden live trap
    • 5 - LOT
    • 6 - Tomahawk
    • 7 - Heslinga
    • 8 - Nest box
    • 9 - INRA trap
    • 10 - None

ANCILLARY ENVIRONMENTAL DATA

In this section, we store the environmental and climatic data empirically collected in the field from the partners. Not all partners have this type of data and they are project-specific, so it is not compulsory to have these data. There are 3 environmental tables that describe the seed productivity "PRODUCTIVITY", the vegetation sampling "VEGETATION" and type of landuse "LANDUSE". Finally also climatic data "WEATHER" is included in this section.

1) PRODUCTIVITY

Please, see template for the table structure. You are invited to use this template to format your data.

  • Sampling date the date when the sampling was performed
  • Acorn the acorn in the plot in grams
  • Berries the berries in the plot in grams
  • Fruits the fruits in the plot in grams
  • Note any specific note on productivity sampling
  • Plot id plot name where productivity monitoring has been performed

2) VEGETATION

Please, see template for the table structure. You are invited to use this template to format your data.

  • Sampling date the date when the samplings were performed
  • Tree species number total number of tree
  • Tree species prevalent the tree species more prevalent
  • Dead trees total number of dead trees
  • Forest origin year of forest origin
  • Woody debris old coarse amount of old wood debris per 100 m2
  • Woody debris fresh coarse amount of fresh wood debris per 100 m2
  • Diameter breast diameter of tree at breast height
  • Shrub species the shrub species more prevalent
  • Herbaceous height (Jan, Mar, May, Jul, Sep, Nov) height herbaceous species in the 6 periods
  • Plot id plot name where vegetation sampling has been performed

3) LANDUSE

Please, see template for the table structure. You are invited to use this template to format your data.

  • Sampling date the date when the samplings were performed
  • Woody plant type of woody plant
  • Canopy height averaged height of canopy
  • Bare soil perc % of bare soil
  • Canopy perc % of canopy cover
  • Deep perc % of deep roots
  • Field layer type of field layer
  • Habitat type of habitat
  • Herbaceous perc % of herbaceous cover
  • Plot id plot name where landuse sampling has been performed
  • Landcover type of landcover
  • Litter perc % of litter ar the ground
  • Rock perc % of rock
  • Shrub perc % of shrub
  • Superficial root perc % of superficial roots
  • Tree layer type of tree layer

4) WEATHER

Please, see template for the table structure. You are invited to use this template to format your data.

  • Sampling date the date when the samplings were performed
  • Sampling time the time (UTC) the samplings were performed
  • Temperature (min, max, mean)
  • Humidity (min, max, mean)
  • Wind speed mean
  • Rainfall sum
  • Snow descriptors 
    • Snow depth
    • Snow cover
    • Snow crust presence
    • Snow more crust presence
    • Snow loose only
    • Ice presence
  • Note any specific note on climate
  • Plot id plot name where climatic sampling has been performed
  • Weather class occurs during sampling 
    Entry number code for weather class:
    • 1 - Sunny
    • 2- Muggy
    • 3 - Cloudy
    • 4 - Overcast
    • 5 - Windy
    • 6 - Low rain
    • 7 - Heavy rain
    • 8 - Snow