Annotation bake-off with SBC datasets and extension

Instructions

1. Use Morpho for semtools (v 1.10 or greater). It will automatically load the SBC OBOE extension from SVN head.

2. When you open a dataset to annotate, duplicate the dataset in your own scope (File->save a copy). Everyone will annotate all the datasets, and Morpho does not yet have a mechanism for handling multiple annotations.

3. Metadata can also be viewed at http://fred.msi.ucsb.edu:8080/knb

Datasets

Datasets are organized by increasing complexity. Original docid is shown, without revision numbers (as these may change). SBC prefixes have been removed from most titles. A short description is included, with the number of columns.

Bottom Temperature

Reed. 2010. Bottom Temperature. mob_semtools.13

http://fred.msi.ucsb.edu:8080/knb/metacat/mob_semtools.13/semtools

One table, 5 columns. Water temperature at 11 sites, by date and time.

Stream Discharge and water temperature at Arroyo Burro Creek, Cliff Drive (AB00)

Melack. 2009. Stream Discharge and water temperature at Arroyo Burro Creek, Cliff Drive (AB00) mobrien.47

http://fred.msi.ucsb.edu:8080/knb/metacat/mobrien.47/semtools

One table, 4 columns

Stream flow and water temperature at one station, with 2 timestamps (local and UTC). station name is in metadata. This group is one of a group of identically formatted datasets which could all share an annotation.

Daily precipitation from station UCSB-200, 1951-ongoing

Melack. 2009. Total daily precipitation from station UCSB-200, 1951-ongoing mob_semtools.19

http://fred.msi.ucsb.edu:8080/knb/metacat/mob_semtools.19/semtools

1 table, 3 columns

Aggregated rainfall from one station, includes date and one flag column

Monthly Kelp wet/dry weight

TBA: part of Reed. 2009. Monthly Kelp CHN, knb-lter-sbc.24

http://fred.msi.ucsb.edu:8080/knb/metacat/knb-lter-sbc.24/semtools

One table, ~9 colums

Kelp dry weight and wet weight by site, date. (TO BE CREATED  from knb-lter-sbc.24)

Santa Cruz Island: Surfperch and Garibaldi

Holbrook, Schmitt. 2010.  Santa Cruz Island: Surfperch and Garibaldi mob_semtools.27

http://fred.msi.ucsb.edu:8080/knb/metacat/mob_semtools.27/semtools

 Four fish were counted at transects off SCI.

Table: 18 columns. date, site, replicate counts (reps in separate rows), several columns of taxonomic classification for each row (result of a join)

Santa Cruz Island: Abundance and biomass of benthic organisms

Holbrook, Schmitt. Santa Cruz Island: Abundance and biomass of benthic organisms (food resource collection) mob_semtools.9

http://fred.msi.ucsb.edu:8080/knb/metacat/mob_semtools.9/semtools

Description TBA

Stream Chemistry in the Santa Barbara Coastal Drainage Area

Melack. 2009. Stream Chemistry in the Santa Barbara Coastal Drainage Area mob_semtools.3

http://fred.msi.ucsb.edu:8080/knb/metacat/mob_semtools.3/semtools

Chemistry from stream water sampled at many locations and dates.

One table, 12 columns

TBD: a second table of sampling sites with lats and lons is available, but not included. Second table could provide context for site column in main table.

Moored CTD and ADCP Data from Arroyo Burro Reef Mooring (ARB)

Washburn. 2010.  Moored CTD and ADCP Data from Arroyo Burro Reef Mooring (ARB) mob_semtools.15

http://fred.msi.ucsb.edu:8080/knb/metacat/mob_semtools.15/semtools

data from a coastal mooring. Many repetitive columns, so this is a very wide table (~80 cols, originally). Hideous, really, but this is the product that the phys-oceanographers share, because it is the most compact final (ie, QC'd) product for an ADCP+CTD mooring. Some important metadata info is stored in text or label fields, so this dataset could really benefit from additional annotation to capture details.

in general, each row is a group of vertical bins for the entire water column that have been transposed, accompanied by data from instruments fixed in the water column: a group of ~16 columns with north-flow, followed by  ~16 columns with east-flow, ~16 columns with errors for north-flow, ~16 columns with errors for east-flow. each of the ~16 cols in a group represents a depth "bin". these cols are followed by 

It would make a better exercise for this group if the ADCP data were reduced to fewer bins. I'll try to get it down to about 20 columns without losing any complexity.

This dataset is one of a group which have nearly identical format (changes: location of the fixed CTD and the size of the ADCP bins).

Nearshore Water Profiles (Monthly CTD and Chemistry) 

Washburn, Siegel, Brzezinski, Carlson, 2010.Nearshore Water Profiles (Monthly CTD and Chemistry) mob_semtools.11

http://fred.msi.ucsb.edu:8080/knb/metacat/mob_semtools.11/semtools

Two tables: each is ~40 columns wide

Table 1: CTD data in 1-meter aggregates.

Table 2: Rosette-sampled chemistry data with "snapshot" CTD values. See image for Ben and Margaret's attempt at a simple context outline.

Tables are definitely NOT context for each other, but are independent observations at the same nominal location (site name).

Net primary production, growth and standing crop of Macrocystis pyrifera

Rassweiler, Arkema, Reed, Zimmerman, Brzezinski,  2009. Net primary production, growth and standing crop of Macrocystis pyrifera in Southern California. mob_semtools.17

http://fred.msi.ucsb.edu:8080/knb/metacat/mob_semtools.17/semtools

Note: This is also an ESA data paper. See metadata for citation. (Took a stab at mapping EML to ESA once, but did not finish).

Three tables.

Table 1:

Table 2:

Table 3:

Beach Wrack Cover

Dugan. 2009. Wrack Cover mob_semtools.29

http://fred.msi.ucsb.edu:8080/knb/metacat/mob_semtools.29/semtools

no table yet - coming soon

Long Term Kelp Removal Experiment: Invertebrate and algal density

Reed. 2010. Long Term Kelp Removal Experiment: Invertebrate and algal density. mob_semtools.__

This experiment has 6 to 8 datasets, with similar data tables - this is only one of the group. The table is being revised, please come back later.