MOD-CO Technical Terms
From Meta-Omics Data of Collection Objects
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Overview on frequently used general technical terms in the MOD-CO project
This glossary "Technical Terms" provides an overview on frequently used general technical terms in the context of the present project. It is open to include all kind of MOD-CO related terms used with reference to general aspects on vocabularies, knowledge information and representation, linked open data, the SQL and relational data base world etc. It supplements the Vocabulary for the MOD-CO schema controlled terms.
| MOD-CO-related term | MOD-CO-related definition | MOD-CO-specific example | Remarks |
|---|---|---|---|
| class | A set or category of things having some related properties or attributes in common, grouped together, and differentiated from others under a general name or description; a kind, a sort. | Classification of preparation methods: preservation, sterilization, isolation, separation, drying, dissection, filtration | - |
| controlled vocabulary | An established list of standardized and defined terminology for use in indexing and retrieval of information. | Physical unit descriptor: physical unit processing <class>. Physical unit descriptor states: gathering, preparation, extraction, amplification ; data unit descriptor: data unit processing <class>. Data unit descriptor states: selection, storage. |
- |
| data flow | Chronological concatenation of individual data records. | DNA sequence, DNA sequence alignment and sequences analysis, sequences deposition in public archive. | - |
| data element | Individual element within an ordered entity in a relational database model | See single cell, e. g., "label" in the Table: Descriptor under http://diversityworkbench.net/Portal/DescriptionsModel_v3.00.14#Table:_Descriptor | - |
| data generation | Creation of information based on measurements, represented in an information artefact (data record) that is understandable by dedicated computational tools that can use the data as input or produce it as output. | Image, measurement data, documentation | - |
| data record | Specification of an individual item in a MOD-CO work and data flow by using defined descriptors. | DNA-sample data including ID (calculated), parent ID (proceeding product ID), and laboratory protocol content (DNA isolation kit, etc.)****- dateneintrag auf der basis des MOD-CO schemas*** | - |
| descriptor | Element with state(s) and value(s) for describing the property or accomplishment of an item. | unit location <value, name>: | - |
| descriptor dependency | The conditional dependence between a categorical descriptor state and the subsequent descriptor in the next higher level. | <presence> or <class> | - |
| descriptor state, value | Specification of descriptors for describing the property or accomplishment of an item. | <presence> or <class> | - |
| digital/data unit | Data object which is described by the MOD-CO schema **** data set , data package and single data record | fasta file, sequence trace image, unit-based specimen record | - |
| digitalization | Transformation of a measurement signal into a digital unit / value. | - | - |
| elementary procedural step | Treatment of an item or measurement of an item (used to achieve a grouping of descriptors within a given schema level). | processing (incl. storage), measurement (incl. digitalisation), data generation | - |
| intermediate | Individudal intermediate ('product') of a work and data flow | - | - |
| item | Physical unit or digital unit ('product'). | fasta file, water sample | - |
| item description | Data record for physical or digital units ('product'). | - | - |
| measurement | Comparative examination ('analysis') of a physical unit. | Salinity measurement, soil acidity measurement, nucleic acid concentration; observation of biotic and abiotic traits | - |
| measurement signal | Electromagnetic or optical impulse of a measurement device as a basis for data generation. | acidometer sensor signal, voltage measurement | - |
| norm (ISO) | ISO (International Organization for Standardization) is an independent, non-governmental membership organization and the world's largest developer of voluntary International Standards. | ISO8601 | - |
| ontology | Explicit specification of a conceptualization, that can exist for an agent or a community of agents | see https://bioportal.bioontology.org/ontologies/ENVO; ecoregions | - |
| physical unit | Physical object | DNA extract, pine needle, sediment core | - |
| processing | Treatment of an item or measurement of an item for achieving a derived product ('item'). | partitioning, treatment, accumulation | - |
| product | Physical or digital unit ('item'). | total DNA extracted from water, metagenomic sequence reads from DNA extract | - |
| property | Declaration of state or value of a given descriptor for generating an item description. | - | - |
| protocol (content) | Structured or unstructured description of one or several procedural steps for achieving a derived *** physical *** product ('item') | Laboratory | - |
| protocol (information technical) | Structured or unstructured description of one or several procedural steps for achieving a derived digital product ('item'). | Phylogenetic tree building steps, i.e. alignment, curation, alignment position filtering, tree algorithm | - |
| relational database model | Representation of data entities in terms of ordered lists of data elements ('tuples'), grouped into relations as part of a relational database. | See entity-relation diagrams of a SQL relational database under http://diversityworkbench.net/Portal/DiversityDescriptions_Information_Models | - |
| schema | Structure of descriptors for generating a data record. | - | - |
| schema level | Collection of descriptors of a given degree of granularity within the schema hierarchy. | - | - |
| schema hierarchy | The structural system in which all level are ranked according to their granularity. | - | - |
| standard (content) | Collection of descriptors structured according to a schema having been accepted by a scientific community in context of a standardization procedure. | ABCD, DwC, MIxS | - |
| standard (information technical) | Collection of specifications that define file formats and file naming. | odt, shp, tiff | - |
| treatment | Unit is modified or altered in some way, but not separated into subunits. | manipulation, purification | - |
| work flow | Concatenation of derived physical or digital units | DNA extraction from a water sample, total mRNA extraction from pine needles collected on field | - |
see also Internal:MOD-CO Schema overview and Internal:MOD-CO Schema controlled vocabulary
