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--- lims-data-structures [2024/03/04 19:14] – 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 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.
+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.
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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 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 substances comprised of or using other substances, e.g. small molecules and monomers synthesized in a reaction using Chemicals, polymers, and so forth, and the resulting product(s) of those syntheses. The real identity of the Material, then, is the intended or primary product.
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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: Connecting the models ===
-Each experimental data entry relates back to information concerning the components, polymers, and/or composites used in the sample 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 component(s), polymer(s), and/or composite in that sample is **required** by the system.  This information is then used to piece together the experimental data entry, which also captures information about the instrumentation used, when it was used, the data category, and other information.
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-Additionally, each experimental data entry requires an experimental identifier (experiment ID).  The experiment ID is analogous to a serial number for the given sample and should be attached to each piece of experimental data in which that sample was used.
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-The workflow would proceed as follows:
-  * 1) synthesize your sample and generate an experiment ID (from either the electronic lab notebook, ELN, or from the LIMS metadata tool)
-  * 2) characterize your sample (e.g. via SAXS/WAXS) and submit the data under that experiment ID
-  * 3) repeat (2) for however many characterization types you perform on that sample