Abalone Data Dictionary

Welcome to the abalone data dictionary! Become familiar with key terms, their format, and purpose in the data collection.

Priority	Header	Type of data	Example	Notes
High	Individual ID	The individuals' ID is ithe date it was spawned followed by its initial tag color and 3-digit number: YYYY_MM_DD_color_###	2017_03_01_orange_867	As our population grows, certain tags might need to be re-used within the engire captive white abalone population; however, I think we can avoid using the same tag twice within animals with the same birthday/spawning day, so this should work as a unique identifier for tagged animals. For animals collected from the wild, the number would be the collection date rather than the date spawned.
High	Tag number(s), date	generally a color, a 3-digit number and dates that tag was on	Green_389 from 3/4/08 to 4/6/15, Green_390 from 4/6/15 to present	Sometimes tags fall off. It can be logistically challenging to give them the same tag, so they sometimes get assigned new tags. Also, occasionally tags have another form besides color_### (e.g., they have 2 or 4 digits and/or have no color associated with them), and sometimes they are something crazy like, "no tag" or "no tag red zip tie" for animals that lived long ago ... though I suppose we could re-code those into something more tractable
High	Shellfish Health Lab Case Number	SF##-##	SF08-25	Animals from each spawning date and from each wild collection have a unique case number created by California's state Shellfish Health Laboratory (SHL). Sometimes animals from a single spawning date have more than one SHL number.
Medium	Cohort	place_YYYY	AOP 2015	This is how we coloquilly refer to each of our populations spawned on a certain date. It's bascially a note/nickname for each group of animals with a particular SHL #/spawning date.
High	Origin	bred in captivity ("captive bred") or collected from the wild ("wild collected")	captive bred, wild collected	Animals were either bred in captivity or collected from the wild
High	Spawning date	date	4/23/01	If animals were collected from the wild, there is no spawning date entered
High	Collection date	date	12/16/17	Only for animals collected from the wild
Low	Generation	F0, F1, F2, F3, etc.	F1	This is a note.
Medium	Potentail parantage	List of potential parents/crosses	Pink_047xGreen_023, Pink_014xPink_188, Pink_024x'no tag', Pink_014x'no tag', Pink_038x'no tag', Pink_047x'no tag'	All of these parents would be in the database by their individual IDs, so we can change our inputed data to reflect this. It would be great if there were a way link to those potential parents to each spawning success date. Otherwise, this is more of a note.
High	Institution	facility, by date range	BML from 6/5/13 - 11/20/14, AOP from 11/20/2014 - present	Animals move around among a finite number of partner institutions (it is possible for new facilities to be added, but it only happens about once every few years). For now, these facilitie are: Aquarium of the Pacific (AOP) Cabrillo Marine Aquarium (CMA) California Science Center (CSC) CICESE Moss Landing Marine Laboratories (MLML) NOAA Southwest Fisheries Science Center (SWFSC) Santa Barbara Museum of Natural History Sea Center (SBMNH SC) The Abalone Farm (TAF) The Bay Foundation (TBF) The Cultured Abalone Farm (TCAF) UC Davis Bodega Marine Laboratory (BML) UC Santa Barbara (UCSB)
Medium	Holding area	tank space by date	Juvenile Rack 1 Column A Trough 3 from 3/4/15 - 6/2/16, Grow Out Tank 3 from 6/2/16 - present	This is a note. The types of input will vary significantly within a facility and over time.
Low	Temperature	temperature, by tank, date, and time	14.3°C on 6/4/15 at 2:13 AM in Juvenile Rack 1 Column A Trough 3	We have temperature loggers that record temp in each Holding area every 30 minutes. It would be cool to link this in here, but low priority. If we can't link it in, it would be nice to have this as a note of what the temperature set point was for that system, (e.g., 14°C, 16°C, or "ambient")
High	Length (mm), by date	number, by date	113.4 on 5/17/11	We sometimes measure every animal within a spawnign date group, and we sometiems only measure a portion of them. When we measure a portion, I'd like it to be possible to predict the size distribution among the whole population within that spawning date group.
Medium	Mass (g)	number, by date	19.63 on 11/6/2014	Length is the most important metric that we record, but mass is also nice to track, and the data collected in the same way as weight.
Low	Shrinkage score	number (0-3), by date	0 on 12/18/2013	This is not a terribly useful metric to track, but we collect the data in the same way as length and weight, so it might be simple to include.
High	Gonad score	number (0-3), by date	1 on 5/2/2013	This is very useful!
High	Predicted sex	male or female, sometimes with uncertainty, by date	M? on 11/2/2015 or F on 10/8/2015	When we take a gonad score, we also try to visually sex the animal. Sometimes we are wrong, which is why we also have the category below, where sex is confirmed by spawning.
High	Confirmed sex (gametes spawned)	male or female (no uncertainty)	M
Medium	Spawning attempt	result of spawning attempt, coded by n, y, or Y (did not spawn, spawned but not many gametes, spawned lots of gametes, respectively), by date	Y on 5/30/2012	For our breeding animals, I'd really like to be able to easily track their spawning success. I'd like to be able to ask questions like, what proportion of animals spawned each year, and how frequently this this particular animal spawn throughout the past decade?
Medium	Eggs spawned	number, by date	345,789 on 5/30/2012 or 20,500,000 on 4/16/19
Medium	Crosses	Tag number of animals that the gametes were crossed with by date	Pink 050 and Yellow 123 on 5/30/2012	This is kind of the same information that is above in "potentail parentage" but from a different perspective -- i.e., linked to the parent instead of the offspring. As above, we can use the individual IDs for this (YYYY_MM_DD_color_###)
Low	Sperm cryopreservation	Date, method used, location	5/30/2012, 20% DMSO, Cherr Lab -80 freezer	This is a note.
High	Mortality	date	5/4/13
Medium	Terminal total weigth	number	15.8	These data are only taken occasionally, so they are not high priority for the MVP.
Medium	Terminal shell weight	number	12.7	These data are only taken occasionally, so they are not high priority for the MVP.
Medium	Terminal shell length	number	16.95	These data are only taken occasionally, so they are not high priority for the MVP.
Medium	Terminal body shrinkage	number (0-3)	3	These data are only taken occasionally, so they are not high priority for the MVP.
Medium	Terminal sex	male, female, or undetermined	M	These data are only taken occasionally, so they are not high priority for the MVP.
Medium	Terminal gonad score	number (0-3)	0	These data are only taken occasionally, so they are not high priority for the MVP.
Medium	Terminal shell condition	notes	Fair condition; possibly some recent polydora penetrations and lots of old ones covered up	These data are only taken occasionally, so they are not high priority for the MVP.
Low	Waxing treatment	date	12/18/13	Waxing treatments occur on a small subset of animals 1-2x per year. They have a single date associated with them.
Low	Oxytetraccyline bath treatmant	date range(s)	11/5/12 - 11/10/12	OTC baths occur occasionally over a range of dates. We could just put the start date of the treatment if that is easier.
Low	Oxytetraccyline feed treatmant	date range(s)	11/5/12 - 11/10/12	OTC feed also occurs over a range of dates. We could also just put the start date of the treatment if that is easier.
Low	CaXc sampling	date and result	8/5/14, negative	This is a note.
Low	Tissue sampling	date, tissue collected, location(s)	8/2/16, foot, SHL -80 freezer rack 3 and SWFSC	This is a note.
Low	Photos	date, image labeled by view (dorsal, ventral, gonad)	4/1/2014, 2014_04_01 SF08-26 Tag_G328 d.JPG
Medium	Experimental manipulation	experiment name, treatment(s), date range	CaXc carryover experiment, high CO2 treatment, CaXc positive treatment, 2/28/19-present	This is a note. The types of input will vary significantly within a facility and over time.