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--- lims-data-structures [2024/03/04 19:42] – csdunham
+++ lims-data-structures [2026/02/13 19:05] (current) – [Instrument-specific Data Models in LIMS] csdunham
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-===== How is data organized in the LIMS? =====
+====== How is Data Organized in the LIMS? ======
+The LIMS system utilizes several data model constructs in order to store data uploaded from the ELN or uploaded to the LIMS directly. All data models ultimately connect to the Experiment data model. Experiment data objects are created and updated for each unique ELN page. These Experiment data objects provide the tracking for any and all protocols, characterization data, and chemical synthesis linked via annotation in any ELN page to the LIMS itself. There are currently over two dozen different data models in the LIMS. A simplified schematic showing how these models relate to each other is shown in Fig 1.
-The LIMS system utilizes several data model constructs in order to generate any experimental data entry. However, there are four (4) data models that are of most significance: chemical, material, experimental data, and well plate.  A simplified schematic is shown in Fig 1.
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-{{:lims_data.png?600|{{:bpm-lims-data-relationships-wiki.png?600|}}
+{{:screenshot_2025-01-21_at_14.15.32.png?600|}}
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-//Fig 1. Schematic illustrating the connections between the data models.//
+//Fig 1. Schematic illustrating some of the connections between data models.//
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+====== Instrument-specific Data Models in LIMS ======
-==== Chemical ====
+Select BioPACIFIC MIP instruments are configured to automatically push data to instrument-specific data models in the LIMS. These instruments, such as the Symphony Peptide Synthesizer and Small Angle X-ray Scattering (SAXS) system, push their data to the LIMS automatically when new data is generated. This data is then parsed by the LIMS and their values are stored in distinct data models in the LIMS database. This provides for simple, rapid, and searchable access to data from these instruments. Furthermore, the data can be readily associated with a user's ELN page(s) via simple point-and-click interfaces in the ELN's **[[eln-guide-basic-page-annotations|instrument annotation modules]]**.
-Chemicals are the simplest classification in the LIMS and represent the lowest level of data complexity.  Any and all chemical species (i.e. reagents and products in a synthetic protocol) belong to the Chemical data model. Each Chemical is assigned a distinct category, such as: monomer, polymer, solvent, catalyst, additional reagent (e.g. surfactants), and so on. The list of chemical categories can be expanded at any time, in accordance with user recommendations and BioPACIFIC MIP needs.
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-Not all fields in the Chemical model are required for user entry; in fact, many of them are optional. Basic information, such as names, formulas, molecular weights, and categories, is required.
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-==== Material ====
-Materials are the next level of data complexity. Materials are defined as any and all Chemicals involved in its synthesis. The real identity of the Material, then, is the intended or primary product species.
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-Key information contained in the Material model include a common name, unique identifier (coming from the corresponding ELN page), synthetic mechanism, and reagent and product chemical species information.
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-==== Experimental Data ====
-Each experimental data entry relates back to information concerning the Materials (and, thus, Chemicals) to which the data applies. This means that each time a piece of data is submitted to the LIMS (e.g. a mass spectrum), information about the Material is **required** by the system.  Thankfully, the ELN helps simplify data entry.
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-Information about Chemicals and Materials is imported into the LIMS through the ELN, via the Import & Upload Data Wizard (Fig 2). All information found in Reagent and Product tables in the ELN gets parsed by the LIMS, and the ELN's unique identifier is also retrieved to link data between the two systems and build the corresponding Chemical and Material data structures within the LIMS database.
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-{{:lims_menu_import.png?600|}}
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-//Fig 2. Highlight of Import & Upload Data in LIMS navigation menu.//
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-After the user makes this connection between the ELN and LIMS in the Import Wizard, the LIMS will ask a series of short questions before arriving at a data upload screen. More about this process will be described in the Tutorial page.