{"id":485,"date":"2017-09-05T10:19:33","date_gmt":"2017-09-05T17:19:33","guid":{"rendered":"https:\/\/mlml.sjsu.edu\/mpsl-mlml\/?page_id=485"},"modified":"2021-12-10T10:42:47","modified_gmt":"2021-12-10T18:42:47","slug":"data-templates-documentation","status":"publish","type":"page","link":"https:\/\/mlml.sjsu.edu\/mpsl-mlml\/data-center\/data-entry-tools\/data-templates-documentation\/","title":{"rendered":"Data Templates and Documentation"},"content":{"rendered":"

Data Templates and Documentation<\/h3>\n
\n\t

Below is a list of all available data templates and documentation for use with the MPSL-MLML Data Center.\u00a0 Data templates are filled out in the laboratory and loaded into the database, usually by the Data Center.\u00a0 Documentation on how to fill out the templates is also available.\u00a0 Check back periodically for the latest version, indicated by the date listed in the table and the date in the file name.\u00a0 Valid values from the MPSL-MLML, CEDEN, and SWAMP databases are also available for reference and the links are listed in the table below.<\/p>\n

File and Batch Naming Conventions<\/strong><\/a> (updated 06\/30\/15<\/em>)
\nA PDF document that describes the recommended MPSL-MLML naming conventions for files and batches.<\/p>\n

<\/a>Analytes and Units per Matrix<\/strong><\/a> (updated on demand<\/em>)
\nA link to the LookUp List page on the MPSL-MLML Data Checker website.\u00a0 Click the Excel logo next to the \u201cAnalyte with Unit per Matrix\u201d link to generate a current Microsoft Excel document that contains the full Analyte List and required reporting units used for the MPSL-MLML database. This list includes all conventional inorganic nutrients, organics (PCBs, pesticides, PAHs, TPHs, VOAs), metals, toxicity, and grain size. The list covers water, sediment, toxicity, tissue, and physical habitat matrices.<\/p>\n

\n

(02\/24\/17<\/em>)<\/span><\/p>\n\n\n\n\n\n\n\n\n\n\n\n\n\n
\n

Data Type<\/strong><\/h4>\n<\/td>\n

\n

MPSL-MLML<\/strong><\/h4>\n<\/td>\n

\n

CEDEN<\/strong><\/h4>\n<\/td>\n

\n

SWAMP<\/strong><\/h4>\n<\/td>\n<\/tr>\n

<\/td>\nLookup Lists<\/a><\/td>\nLookUp Lists<\/a><\/td>\nLookup Lists<\/a><\/td>\n<\/tr>\n
Vocabulary Request<\/strong><\/td>\n<\/td>\n<\/td>\nTemplate<\/a>
\n(01\/08\/19<\/em>)<\/span><\/td>\n		<\/td>\n<\/td>\n<\/td>\n<\/tr>\n
Project Registration<\/strong><\/a><\/td>\nDocumentation
\n(contact Help Desk<\/a><\/em>)<\/span><\/td>\n		<\/td>\n<\/td>\n<\/td>\n<\/td>\n<\/tr>\n
Station<\/strong><\/a><\/td>\nTemplate<\/a>
\n(06\/30\/15<\/em>)<\/span><\/td>\n		Documentation
\n(contact Help Desk<\/a><\/em>)<\/td>\n		<\/td>\n<\/td>\n<\/td>\n<\/td>\n<\/tr>\n
Field\/Habitat<\/strong><\/a><\/td>\n<\/td>\n<\/td>\n\n

Template<\/a>
\n(01\/08\/19<\/em>)<\/p>\n

Example<\/a>
\n(01\/08\/19<\/em>)<\/p>\n<\/td>\n

Documentation<\/a> (01\/08\/19<\/em>)<\/td>\nTemplate<\/a> (03\/15\/13<\/em>)<\/p>\n

Benthic\/BA Example<\/a><\/p>\n

WQ Example<\/a><\/td>\n

<\/td>\n<\/tr>\n
Water\/Sediment Chemistry<\/a> <\/strong><\/td>\n<\/td>\n<\/td>\n\n

Template<\/a>
\n(01\/08\/19<\/em>)<\/p>\n

Example<\/a>
\n(01\/08\/19<\/em>)<\/p>\n<\/td>\n

Documentation<\/a> (01\/08\/19<\/em>)<\/td>\nTemplate<\/a> (08\/21\/13<\/em>)<\/td>\nDocumentation<\/a> (01\/26\/15<\/em>)<\/td>\n<\/tr>\n
Tissue Chemistry<\/a><\/strong><\/td>\n<\/td>\n<\/td>\n\n

Template<\/a>
\n(01\/08\/19<\/em>)<\/p>\n

Example<\/a>
\n(01\/08\/19<\/em>)<\/p>\n<\/td>\n

\n

Documentation<\/a> (01\/08\/19<\/em>)<\/p>\n<\/td>\n

Composite Template<\/a> (08\/21\/13<\/em>)<\/p>\n

Results Template <\/a>(08\/21\/13<\/em>)<\/td>\n

Documentation<\/a> (06\/23\/09<\/em>)<\/td>\n<\/tr>\n
Toxicity<\/strong><\/a><\/td>\n<\/td>\n<\/td>\n\n

Template<\/a>
\n(01\/08\/19<\/em>)<\/p>\n

Example<\/a>
\n(01\/08\/19<\/em>)<\/p>\n<\/td>\n

\n

Documentation<\/a> (01\/08\/19<\/em>)<\/p>\n<\/td>\n

Template <\/a>(11\/13\/14<\/em>)<\/td>\nDocumentation<\/a> (11\/13\/14<\/em>)<\/td>\n<\/tr>\n
Taxonomy<\/strong><\/a><\/td>\n<\/td>\n<\/td>\n\n

Template<\/a>
\n(01\/08\/19<\/em>)<\/p>\n

Example<\/a>
\n(01\/08\/19<\/em>)<\/p>\n<\/td>\n

\n

Documentation<\/a>\u00a0 (01\/08\/19<\/em>)<\/p>\n<\/td>\n

Template <\/a>(10\/10\/13<\/em>)<\/td>\nDocumentation<\/a> (<\/span>10\/20\/10<\/em>) <\/span><\/td>\n<\/tr>\n
Time Series<\/strong><\/a><\/td>\nTemplate<\/a>
\n(08\/01\/14)<\/td>\n		Documentation
\n(contact Help Desk<\/a><\/em>)<\/td>\n		<\/td>\n<\/td>\n<\/td>\n<\/td>\n<\/tr>\n<\/tbody>\n<\/table>\n<\/div>\n<\/div><\/div>
\n\t\t\t\t\t\t\t

\n\t\t\t\t\t\tPrior to Sampling\t\t\t\t\t\t<\/h1>\n\t\t\t\t\t\t<\/div>\n<\/div><\/div>
\n
\n\t

Project Registration\u00a0 <\/a><\/h3>\n

The Project Registration template helps users compile the new project information needed to initially create project specific codes including Agency, Station, Collection Device, QAPP, Sampling Protocol, Program, and Project.\u00a0 The information supplied in the template is used by the MPSL-MLML Data Center to create new codes in the database that are essential for data comparability and will allow the user to add associated data to the MPSL-MLML database.\u00a0 Once the information is compiled, contact the MPSL-MLML Help Desk<\/a> to have the individual codes created.\u00a0 Documentation on how to fill out the template is also available. Please contact Stacey Swenson<\/a> for more information.<\/p>\n

The Station template contains specific information related to the station (e.g., StationCode, Waterbody, County) which allows for stations to be categorized by geographic area. This provides continuity and consistency among tables within the database. Documentation is also available that describes the process for for filling out the template and reporting station data.<\/p>\n

It is critical that this template be completed prior to sampling and loaded into the database so that laboratory results are correctly loaded to the database.\u00a0 Zip files containing GIS Shapefile Layers<\/a> are available for use in software such as ArcGIS to help populate fields associated with CalWater, Counties, Ecoregion, HBASA, and NHD.\u00a0 An Excel file under the CalWater section on the GIS Shapefile Layers page is also available to help populate specific fields if the corresponding CalWater information is known. If you have any questions concerning these files, contact Marco Sigala<\/a>.<\/p>\n<\/div>\n<\/div><\/div><\/div><\/div>

\n\t\t\t\t\t\t\t

\n\t\t\t\t\t\tField Submissions\t\t\t\t\t\t<\/h1>\n\t\t\t\t\t\t<\/div>\n<\/div><\/div>
\n
\n\t

<\/a>Using field data sheets that contain all the necessary information for field data entry may be helpful and speed up the process of submitting data templates to the MPSL-MLML Data Center.\u00a0 Field Data Sheets<\/a> that may be used include Water Quality, Tissue, and Bioassessment.<\/p>\n

<\/a>Field\/Habitat Collection and Results Template<\/h3>\n

(Field\/Habitat\/Benthic\/Bioassessment\/Algae Collections <\/strong>& Field\/Habitat Results)<\/strong>
The file contains multiple worksheets, including FieldResults and HabitatResults, with the appropriate fields required to load historic and current field and habitat results into the database.\u00a0 While this template was developed for loading SWAMP Bioassessment data following the SWAMP Wadeable Streams protocol, it can be used for loading all water quality and bioassessment sampling data into the MPSL-MLML database.\u00a0 A data submission example is included in the CEDEN template and documentation provides detailed guidance to assist data providers in preparing and submitting data using the Field\/Habitat Collection and Results data template.\u00a0 For the SWAMP template, a Benthic\/Bioassessment and a Water Quality Example of a completed Field Collection and Results Template is available for reference.\u00a0 Documentation may be forthcoming.<\/p>\n

The Bioassessment Analyte and Location Crosswalk<\/a>\u00a0is also available to help the user populate the correct constituent parameters for corresponding analytes and locations.<\/p>\n

Additional Tools<\/a> are available for Bioassessment Field Data Entry.<\/p>\n

Back to Top<\/a><\/p>\n<\/div>\n<\/div><\/div><\/div>

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\n\t\t\t\t\t\tLaboratory Submissions\t\t\t\t\t\t<\/h1>\n\t\t\t\t\t\t<\/div>\n<\/div><\/div>
\n
\n\t

Chemistry Data\u00a0 <\/a><\/h3>\n

The template contains worksheets for reporting chemistry results and lab batch data to the MPSL-MLML Data Center, with the appropriate fields required to load chemistry data into the database including nutrients, metals, organics, inorganics, and bacteria data.\u00a0 A data submission example is included in the Excel file.\u00a0 Documentation is available to provide detailed guidance to assist data providers in preparing and submitting data using the chemistry data template.<\/p>\n

\u00a0<\/h3>\n

Toxicity Data\u00a0 <\/a><\/h3>\n

The template contains worksheets for reporting toxicity summary, replicate, and batch data to the MPSL-MLML Data Center.\u00a0 A data submission example is included in the template.\u00a0 Documentation is available to provide detailed guidance to assist data providers in preparing and submitting data using the toxicity data template.<\/p>\n

\u00a0<\/h3>\n

Tissue Data\u00a0 <\/a><\/h3>\n

The MPSL-MLML database is designed to store data elements for analyses of fish, bivalve, bird, and mammal tissue.\u00a0 Templates for both tissue collection data and tissue results are available.\u00a0 A data submission example is included in the template.\u00a0 Documentation is available to provide detailed guidance to assist data providers in preparing and submitting data using the tissue data templates.<\/p>\n

\u00a0<\/h3>\n

Taxonomic Data <\/a><\/h3>\n

The template for submitting lab effort and species results data to the MPSL-MLML Data Center also contains a BenthicResults worksheet with appropriate fields required to load benthic data into the database.\u00a0 Macro invertebrates, Marine Infauna, and Algae Abundance data should also be submitted using this template.\u00a0 A data submission example is included in the template.\u00a0 Documentation is available to provide detailed guidance to assist data providers in preparing and submitting data using the taxonomy data template.\u00a0 The current MPSL-MLML OrganismLookUp list values for SAFIT Benthic Macroinvertebrate (BMI)<\/a> and CAD-TWG Soft Algae<\/a> taxa are also available.\u00a0 Use the following\u00a0links for taxonomic reference:<\/p>\n

Marine<\/strong> \u2013 SCAMIT<\/a> So. California Association of Marine Invertebrate Taxonomists
Freshwater BMI<\/strong> \u2013 SAFIT<\/a> SW Association of Freshwater Invertebrate Taxonomists\u00a0<\/p>\n

Time Series Data <\/a><\/h3>\n

The MPSL-MLML database is designed to store data elements for time series (continuous monitoring) field data.\u00a0 A data submission example is included in the template.\u00a0 Documentation is available to provide detailed guidance to assist data providers in preparing and submitting data using the time series data template.<\/p>\n<\/div>\n<\/div><\/div><\/div><\/div><\/div><\/div>","protected":false},"excerpt":{"rendered":"

Below is a list of all available data templates and documentation for use with the MPSL-MLML Data Center.\u00a0 Data templates are filled out in the laboratory and loaded into the database, usually by the Data Center.\u00a0 Documentation on how to fill out the templates is also available.\u00a0 Check back periodically for the latest version, indicated […]<\/p>\n","protected":false},"author":15,"featured_media":0,"parent":481,"menu_order":2,"comment_status":"closed","ping_status":"closed","template":"","meta":{"footnotes":""},"categories":[],"tags":[],"class_list":["post-485","page","type-page","status-publish","hentry"],"distributor_meta":false,"distributor_terms":false,"distributor_media":false,"distributor_original_site_name":"Marine Pollution Studies Laboratory at MLML","distributor_original_site_url":"https:\/\/mlml.sjsu.edu\/mpsl-mlml","push-errors":false,"_links":{"self":[{"href":"https:\/\/mlml.sjsu.edu\/mpsl-mlml\/wp-json\/wp\/v2\/pages\/485","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/mlml.sjsu.edu\/mpsl-mlml\/wp-json\/wp\/v2\/pages"}],"about":[{"href":"https:\/\/mlml.sjsu.edu\/mpsl-mlml\/wp-json\/wp\/v2\/types\/page"}],"author":[{"embeddable":true,"href":"https:\/\/mlml.sjsu.edu\/mpsl-mlml\/wp-json\/wp\/v2\/users\/15"}],"replies":[{"embeddable":true,"href":"https:\/\/mlml.sjsu.edu\/mpsl-mlml\/wp-json\/wp\/v2\/comments?post=485"}],"version-history":[{"count":51,"href":"https:\/\/mlml.sjsu.edu\/mpsl-mlml\/wp-json\/wp\/v2\/pages\/485\/revisions"}],"predecessor-version":[{"id":1370,"href":"https:\/\/mlml.sjsu.edu\/mpsl-mlml\/wp-json\/wp\/v2\/pages\/485\/revisions\/1370"}],"up":[{"embeddable":true,"href":"https:\/\/mlml.sjsu.edu\/mpsl-mlml\/wp-json\/wp\/v2\/pages\/481"}],"wp:attachment":[{"href":"https:\/\/mlml.sjsu.edu\/mpsl-mlml\/wp-json\/wp\/v2\/media?parent=485"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"https:\/\/mlml.sjsu.edu\/mpsl-mlml\/wp-json\/wp\/v2\/categories?post=485"},{"taxonomy":"post_tag","embeddable":true,"href":"https:\/\/mlml.sjsu.edu\/mpsl-mlml\/wp-json\/wp\/v2\/tags?post=485"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}