v25 BMS Glossary
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Accession, Genebank | In a genebank, accessions are the key genetic entities. An accession is the genetic unit of maintenance, responsibility, exchange, distribution, and intellectual property. | Genebanks uniquely identify accessions within their collection through Accession IDs (numbers, names). Recipients of germplasm from a genebank identify the germplasm they need by Accession ID and its characteristics, and are expected to use the Accession ID to identify the germplasm in their publications. Just as a seed company seeks to maintain the genetic identity of an improved variety, so a genebank seeks to maintain the genetic identity of an accession despite repeated cycles of propagation. Information on the origins of an accession and on any conditions governing its use remain unchanged over cycles of propagation. As part of the process of maintaining the genetic identity of an accession, genebanks need to track the cycles of propagation. An accession is thus a set of germplasm records in a management neighborhood. It consists of a group founding record (group founder) and all germplasm records produced from the group founding record through germplasm maintenance methods under the management of the genebank. Effective management of an accession depends on maintaining 1 GID for each germplasm record in the accession. For any GID representing a germplasm record in a Management neighborhood BMS explicitly use the GID of the group founding record as an indicator of membership in that management neighborhood. All germplasm records that belong to an accession have an associated GID (Group ID) that points to the record of the founding germplasm. This is necessary, since the passport data are connected to the founding germplasm, but need to be linked to all germplasm sample records in the accession. However, in many cases, particularly for accessions received from other collections, a collection manager may have no information on the individual records that comprise the management neighborhood of the donor’s accession. In these cases, one GID is used to represent the entire management neighborhood of the accession, not just its founding record. |
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API, Application Programming Interface | is a way for two or more computer programs to communicate with each other. It is a type of software interface, offering a service to other pieces of software. See BrAPI. | For accessing the list of current API calls, after logged in BMS, redirect the web browser to: “https://www.yourbms.net/bmsapi/“ | Example of BMS calls for GET, POST, PUT and DELETE the method of a variable: 
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Augmented Randomized Block Design (ARBD) | is a experimental standard design where control (check) treatments augmented with new (test) treatments in a complete or incomplete block setting. | BMS can generate Augmented Randomized Complete Block Design (ARCBD) where test entries are replicated once in the design and check/s entry/ies appear once in each block. |
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Blocking Factor | See Replicate factor. |
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BrAPI | BrAPI is a Standardized RESTful Web Service API Specification for plant breeding data. See API. | For more info: BrAPI site |
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Breeding Management System (BMS) | The Breeding Management System (BMS) is an information management system developed by the Integrated Breeding Platform to help breeders manage the breeding process, from project planning to decision-making. |
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Breeding Method (BM), Germplasm | is the method of creation of a germplasm record. Breeding methods describe the modification of germplasm over cycles of crossing, selection, or propagation. A critical distinction in the BMS model is whether a given method is intended to (i) increase, (ii)reduce or repartition, or (iii) maintain genetic variation as measured by allelic or gametic diversity. These three options lead to classifying methods as generative, derivative, or maintenance, respectively. | For practical purposes the BMS include not only breeding methods but also breeding strategies and mating designs for describing the creation method for a germplasm record. Different crops will have different relevant breeding methods, depending on propagation biology - self-pollinated, open-pollinated, or clonally propagated. Breeding, as described by database breeding methods, creates genetic change and necessitates the assignment of new GIDs to the newly created germplasm. For more details see generative BM, derivative BM, maintenance BM, breeding strategy and mating design.
A Conceptual Model for Describing Processes of Crop Improvement in Database Structures. Available from: https://www.researchgate.net/publication/43288607_A_Conceptual_Model_for_Describing_Processes_of_Crop_Improvement_in_Database_Structures | 
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Breeding Strategy | See Breeding Method. | Breeding Strategy, Breeding Method and Mating Design |
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Breeding View (BV) | Breeding View (BV) is a statistical analysis software that accompanies the BMS. BV is a collaboration with between the Integrated Breeding Platform and VSNi, the makers of the Genstat statistical package. BV is an extremely user friendly statistical software that allows breeders to quickly access their results. Trial data exported from the BMS is perfectly formatted for analysis by BV. | Single site analysis: Breeding View Standalone - Single Field Trial Analysis - BMS Manual Breeding View Standalone - Single Field Trial Analysis - Video Genotype by Environment Analysis: Breeding View Standalone - GxE Analysis - BMS Manual Breeding View Standalone - GxE Analysis - Video Breeding View Standalone - GxE Analysis - BMS Tutorial (Step by step) | Breeding View can be installed on computers running the Windows operating system. You must have administrative access to your computer to install BV. If your institution controls your computer's administrative access, you will need to contact your IT department for assistance. The Breeding View App for statistical analysis may be downloaded from: https://www.dropbox.com/s/pga4ks8xxu44wix/BreedingView-1.8.0.4.msi?dl=0 (A detailed step by step of BV installation can be found in BMS manual at this link) |
Coefficient of Parentage (COP) | Also known as the Coefficient of Kinship measures the genetic relationship between strains of germplasm according to the proportion of identical alleles that they share by descent through their pedigrees. COP values are therefore important measures of genetic diversity. | BMS can trace genotypes back to their parental landraces or to lines of unknown pedigree. Genealogical features of a set of germplasm can be exploited through statistics such as the COP. Originally developed by Wright (1922), the COP for two genotypes estimates the expected percentage of alleles identical by descent at loci which are polymorphic within a population. The COP between two lines is the inbreeding coefficient of their offspring. St. Martin (1982) adapted COP analysis to inbred crops by assuming that each genotype is completely homozygous, that genotypes without common parentage are unrelated and that parents contribute equally to the offspring, despite inbreeding and selection. Highly selected, qualitative loci would not follow the assumption of random transmission of a large number of alleles. However, in a general sense, a COP is a measure of overall common ancestry of two genotypes and estimates latent genomic diversity that is not obvious until a crop is challenged by the appropriate biotic or abiotic stress. Breeders can use COPs to increase genetic diversity by selecting lines for crossing with divergent parentage. However, please heed the warning that SPURIOUS LOW COP VALUES THAT REFLECT INCOMPLETE PEDIGREE INFORMATION RATHER THAN A TRUE LOW LEVEL OF COANCESTRY MAY BE GENERATED. If the highest theoretical contribution (HTC) of any ancestor is large (say larger that 0.1) then this may indicate incomplete pedigree information. The HTC corresponds to the first and largest value of the mendelgram and a value of 0.5 usually reflects that one immediate parent is non-expandable, with 0.25 indicating one unexpandable grandparent. The algorithm used for COP computation is described in Sneller (1994).
BMS Instance administrator, in the Parameters tab at the Crop Administration Module, must configure breeding type (BTYPE) parameter according with the crop species (0=cross fertilizing (CF) crops, 1=self fertilizing (SF) crops, 2=self fertilizing with unknown source but known parents). Original sources are assumed unrelated and homozygous in SF crops. For CF species the assumption used to be that all terminal strains were F1s - seeds from a single cross. This proved to be too restrictive for the variety of situations which arise in maize breeding. In particular, lines extracted from a population are much more diverse than lines from a single cross. The generation where sister lines diverge is retrieved from the DB, but where this information is unknown they are assumed to be identical for SF crops or to diverge at the group for CP crops. -Wright, S. 1922. Coefficients of inbreeding and relationship. American Naturalist 56:330-338. -St. Martin, S.K. 1982. Effective population size for the soybean improvement program in maturity groups 00 to IV. Crop Science 22:151-152. -Sneller, C.H. 1994. Pedigree analysis of elite soybean lines. Crop Sci. 34:1679–1680. | COP analysis is executed in BMS by selecting entries on a open list from the germplasm manager.
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Composite Cross Name
| Composite Cross Name is a string containing two or more parental names each separated by a cross symbol. | Within a composite cross name the female parent is always displayed to the left of the cross symbol and the male parent to the right (each parent may be identified by a simple or composite cross name). See Cross. | Composite Cross Name: Bluebird/Supreme |
Crop | Crop is the species name or common name of the crop assigned to BMS DB. | Depending on organization/user needs a single BMS instance may hold one or multiple Crop DBs. | BMS has been implemented for breeding programs working with: Amaranth, Bambara Groundnut, Barley, Brachiaria, Cacao, Camelina, Cannabis/Hemp, Canola, Cassava, Castor bean, Chickpea, Citrus/Lemon, Coconut, Coffee, Common Bean, Cotton, Cowpea, Date Palm, Faba Bean, Field Pea, Finger Millet, Groundnut, Lablab, Lentil, Loblolly Pine, Lupin, Maize, Mango, Marigold, Mung Bean, Napier grass, Oat, Passion Fruit, Pearl Millet, Pigeon Pea, Potato, Quinoa, Rice, Salicornia, Sesame (Simsim), Slash Pine, Sorghum, Soybean, Stevia, Sugarcane, Sunflower, Sweet Potato, Tef, Tepary Bean, Tobacco, Tomato, Wheat, Yam |
Cross Code | Cross Code is a germplasm coded name that uniquely identified a cross. BMS may generate a code to uniquely identified a cross using a rule of syntax. It is also known as Breeder’s Cross ID (BCID). | BMS offers customization for syntax of cross codes to be stored as Cross Name (CRSNM) name type. Cross code = Prefix + Count + Suffix Prefix = Crop and/or Program Identifier Count = is a sequence number identifying an individual cross. Suffix = may content a Cross Type Identifier or a Project Identifier) BMS allow to use Process Codes to insert info into the different parts of the Cross Code. Location abbreviation, cross objective, type of cross, year and season, breeder initials are typical included info on the code construction. | Cross Code: IB01234S Simple Cross Name: TRAFUL Composite Cross Name: Bluebird/Supreme |
Cross Name (CRSNM) | Cross Name is the germplasm name type that store a given name of a cross. The cross name may be a coded name (see Cross Code), a single name (see Simple Cross Name), or it may be a composite name (see Composite Cross Name) containing previously defined simple cross names, each of which is separated from other simple cross names by a cross symbol. | By default BMS is configure to create and store a Cross Code as Cross Name. BMS use an algorithm to produce the Composite Cross Name displayed in the Cross column at tables in the Germplasm, List and Study managers. (see Cross and Cross Code)
| Cross Code: IB01234S Simple Cross Name: TRAFUL Composite Cross Name: Bluebird/Supreme |
Cross (Cross column in BMS UI tables) | Cross is a string containing the composite cross name of a germplasm describing its pedigree. See Cross Name, Composite Cross Name, Cross Symbol, Pedigree. | The cross string describes the parents and crossing sequences used to produce the germplasm. BMS can execute an algorithm for cross expansion to higher levels. The expansion algorithm follows a modified syntax and semantic rules from Purdy Method for pedigree notation. Purdy et al (1968). A Proposed Standard Method for Illustrating Pedigrees of Small Grain Varieties. | Level 1 expansion: Single Cross: A/B Three-Way Cross: A/C//C Two-Way Cross: A/B//C/D Back Cross: A*/B ; A*2/B ; A*3/B
Level 2+ expansion: A/B//C///D Y/4/D*3/A///C//B |
Cross Symbol | Cross symbols are used to separate simple cross names within a composite cross name. The cross symbol indicates either a simple cross or a back cross. Taken as a group the cross symbols in a composite cross name explicitly indicate the order in which crosses were made. | Simple cross symbols are the slash, ’/’, indicating a first order cross; double slash marks; ’//’, indicating a second order cross; ’///’, indicating a third order cross or a single slash mark followed by a natural number ’n’ and a second slash mark (/4/, /5/,…, /n/). The number ’n’ indicates a cross of order ’n’ and is used for fourth order crosses and higher. Higher numbers indicate more recent crosses in the sequence. The most recent or final cross used to create a cultivar is indicated by the highest number within the pedigree. Back cross symbols are composed of an asterisk, ’*’, a natural number and a simple cross symbol. The asterisk separates the name of the back cross parent from the natural number. The natural number identifies the number of times the back cross parent was used. If the asterisk is on the left side of the simple cross symbol, then the back cross parent is the female. If the asterisk is on the right side of the simple cross symbol, then the back cross parent is male. A back cross symbol contains exactly one asterisk. |
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Dataset |
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Data point (Observation or sub-observation on a study) | The central entity in the BMS data model is the datum, which is linked to exactly one unit of observation (or subobservation) and exactly one variable/one germplasm. The data is conceptually equivalent to an intersection of a variable column and a row of a germplasm entry in a spreadsheet or field book. The most important attribute of a datum is its value, which is the recorded value of the associated variable for the unit of observation associated with a germplasm. |
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Derivative Breeding Method | Derivative methods applied to a source progenitor or population (single GID), decrease or redistribute allelic diversity, such as through inbreeding and self-pollination. |
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Derivative Name (=Selection History) | Derivative Name is the germplasm name type that stores the selection history of the germplasm. (See Standard Selection History and Non Standard Selection History) | BMS via customization generate standardized selection histories. Selection History= Cross Code + Selections terms (see Cross Code and Selection Term) Selection History Semantics The semantic interpretation of selection histories is relatively straight forward. The cross code should be unique for any given cross made. The selection terms (steps) may identify the nursery, family, plant, seed, location and/or type of selection made from a segregating population. The order and number of the selection terms is important. The first term identifies the selection made from the F1 generation. Later terms identify later filial generations and the selections made on them. In general, the selections are made in successive generations. However, there are exceptions, particularly in the case of re-selections. Relationship Between Cross Name and Selection history Normally a selection history uniquely identifies a cross and a particular set of selections made on the progeny of the cross. The selection history does not explicitly indicate the parents involved in making the cross. In general, the cross name that corresponds to the cross identifier part of a selection history identifies parents by name and order of crossing to some arbitrary level. However, none of the selection history is conveyed by the cross name itself. There is a one-to-many relationship between cross names and selection histories. In other words, each cross name may have associated with it several selection histories. A selection history will have exactly one cross name associated with it. | Cross Code + Selection terms C00234-B-B-3-12-M-4 |
Derivative Neighborhood, Germplasm | All germplasm records produced from the Group Source (root) germplasm record through either derivative or maintenance germplasm creation methods form a derivative neighborhood.
| It is a germplasm query to list closely related germplasm, users may display it from the Pedigree tab from each Germplasm Record. Starting from a germplasm record anywhere in the derivative neighborhood and tracing back and forth between records linked by derivative and maintenance methods will eventually cover the whole derivative neighborhood. However nested subsets of this neighborhood derived by limiting the number of steps forward or backward in genealogy provide interesting neighborhoods and we call these 'n step derivative neighborhoods' where n is the limit on the number of steps. It should be noted for BMS databases with historical international germplasm records that a derivative neighborhood may contain a number of maintenance neighborhoods, and the germplasm records in it may be held by more than one organization. | The Derivative Neighborhood Query in the Pedigree tab will list all derivative/maintenance relatives of the germplasm record within n (backward and forward) derivative and maintenance steps.
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Designation, Germplasm | is the preferred name of the germplasm at the time of the list, sample or study creation. (see preferred name) |
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Entry | is each germplasm participating in a Germplasm List and/or a study. |
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Entry List Order (ELO) | is a distribution of the germplasm entries in a experimental design that consider their order number in the germplasm list. |
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Entry Type | is a role class assigned to each germplasm used in a study, determined by study objectives. | By default in BMS, all germplasm entries being evaluated in the study are assigned with type 'Test entry’, however a set of germplasm may be specified as other entry types. Their presence and the way they are incorporated in the study are determined by the objectives. For example, a study evaluating elite lines resistance to a disease might include three entry types: “test entry” for the standard germplasm being evaluated, disease resistant and disease susceptible entry types for the controls. | T= Test entry C= Check entry D= Disease check entry DS= Disease susceptible check entry DR= Disease resistant check entry F= Filler LC= Local check S= Stress check X= Non Replicated |
Environment, Study | is each single instance of a study. In BMS a study may contain a single or multiples environments. The “Environment” concept in BMS corresponds to the "Study" concept in MIAPPE and BrAPI, “Field” concept in Fieldbook App and “Occurrence” concept in EBS, other systems or Apps may use Instance, Site, Location as similar concept. |
| Environment = Instance (Location + Season + Conditions) |
environmental factors and details |
| Measurements at the Environment (Study Instance) level In this category we include all observations that are made to characterize the study instance as a whole. For example, its location and other site particulars would be included here. Basic environmental data on the study instance should in fact be recorded routinely. The possibility of genotype by environment interaction highlights the fact that the relationship among different germplasm entries may depend on each particular environment in which the study was conducted. Interpretation and use of the results therefore need some indication of each particular environment under which the study was carried out. Also included here could be indications of the methodologies and practices used for collecting data, and the people involved. |
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Experimental Design | refers to the experimental technique of random assignment/placement of the treatments to the experimental units. | The BMS may generate different experimental single and multi-factorial designs using its own design engine. Also BMS will accept any externally generated design via import of design template file with the arrangement of treatments on experimental units. | BMS may generate:
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Experimental Field Layout | is the physical arrangement of experimental units in space. |
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Experimental Unit
| is the unit to which the treatment or combination of treatments are applied. See Plot. |
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Factors, Experimental | is any experimental parameter (e.g., germplasm entry, irrigation). “Levels” of factors (valid entries) are usually controlled by an experimenter, or else they are imposed by a situation (e.g., planting date). Factors and response variables tend to get mixed up when they appear as parallel columns in a spreadsheet, and a factor in one study (e.g., harvest date) might be equivalent to a trait variable in another study. | Factors in BMS studies: First we need to clarify the meaning of the following basic terms, which are used throughout this guide and which are sometimes confused: -treatments -factors -factor levels -response variables We consider three illustrative examples:
These three studies all have 24 treatments. In the first, there is just a single factor, germplasm, which has 24 levels. Thus, in this simple case, whether we think of the different germplasm entries as the treatments, or the levels of a treatment factor makes no difference. In the second study there are 2 factors, namely germplasm, with 8 levels, and fertilization rates, with 3 levels. Each treatment consists of the combination of a particular germplasm entry and a particular fertilization level. Thus, there are 24 different combinations, or treatments. This is sometimes known as an 8 by 3 factorial treatment structure. The third study has 3 factors and the 24 treatments are arranged in a 4 by 3 by 2 factorial treatment structure. For the 3 studies the evaluated response variable is grain yield. |
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Generation History, Germplasm | is the list of germplasm records on the direct derivative and maintenance path from Group Source (i.e. cross of origin) to actual germplasm. |
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Generative Breeding Method | Generative methods increase allelic diversity by combining alleles from different progenitors, such as crossing, mutagenesis, and transformation. | The germplasm creation may involve one, two or more direct progenitors: One: methods related to mutagenesis, transformation and gene editing technologies. Two: single cross, double cross, backcross, three way cross More than two: polycross Note: this descriptions consider the last generative breeding method used for the creation of the germplasm, for example a three way cross consider two progenitors as the cross between a F1 with another germplasm, expanding to the next cross level a three way cross has 3 progenitors. |
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Germplasm | is the fundamental genetic resource unit of plant breeding and is the common element to almost all relationships in the BMS database. (see Germplasm ID) | A germplasm record can be thought of as a packet of seeds or other propagating material that is managed separately from other such packets of seeds in a collection, in the sense that germplasm specialists would not want to mix them. A new germplasm record is created from an existing record when any one of the following events occurs: -A fresh lot of seed or other propagules is harvested (e.g. seeds from a plot, farmer’s field or natural ecosystem). Each cycle of propagation involves a certain amount or probability of genetic change by mutation, drift, selection (deliberate or unintentional) and/or introgression. Even pure lines may change genetically during propagation, and therefore successive generations of propagation should not be mixed; instead they must be treated as distinct samples. In BMS a new germplasm record is register in the database with a GID when:
| Packet of seeds, plants in a plot on the field, a plant in a pot in the greenhouse, a cloned stake or tissue culture in the lab, a variety, a cultivar, a land race, a line, a breeding stock, a population, a collected wild form, a gene bank accession are all examples of a germplasm record. |
Germplasm Breeding Method | is the germplasm creation method, concept that is biologically motivated. It is called "Breeding Method" in BMS documentation and applications. It describes the method by which the germplasm identified by a GID was created from its most recent known progenitor, which may be the immediate parents or an unknown number of generations before. | Based on the intended change of genetic diversity from parent to offspring, we distinguish three classes of Germplasm creation methods: -Generative germplasm creation methods (intend to increase genetic diversity, e.g. cross) |
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Germplasm ID (GID) | is an auto-incremental unique numeric identifier assigned to all germplasm in the crop database. It is a BMS database internal differentiating identifier. See Germplasm Universal Unique ID and Germplasm Permanent Unique Identifier. | GIDs allow breeders to re-name or assign alternate names to germplasm without changing the database identifier and disrupting the continuity of data relationships. GIDs can refer to an individual with a single genotype or a genetic population with multiple genotypes. | |
Germplasm Attribute | Attributes are variables used to store information about the genesis, genealogy, nomenclature, or chronology of germplasm. | Attributes are flexible user-definable data fields. Attribute types are defined and described as USER_DEFINED_FIELDS. Like names, attributes may contain imbedded information in the form of subfields or variables within the attribute text. A scale identifier specifies the units in which the attribute are required and links attributes to the controlled vocabulary of properties, scales, and methods. |
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Germplasm Descriptor |
| its various feature or descriptors may be recorded for each germplasm record |
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Germplasm Immediate Source | Immediate Source: most recent ancestor |
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Germplasm Name | is a label that identified a germplasm record. Germplasm collects a multitude of labels during the development and release process. |
| Germplasm Bank Accession Number (ACCNO); Cross Name Unnamed cross (CRSNM); (UNCRS); Release Name (RELNM); Derivative Name (DRVNM); Variety Name (VARNM); Code Name (Code1, Code2, Code3), Line Name (LNAME); Selection History at Fixation (SELHISFIX), Pedigree (PED) |
Germplasm Passport |
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Germplasm Permanent Unique Identifier (PUI) | is a persistent, unique identifier assigned to the germplasm record so it can be unambiguously referenced at the global level and the information associated with it. It is a BMS database external aggregating/unifying identifier. | Germplasm PUI are stored as a Name Type in BMS DB, its generation is external. For example, a DOI may be stored as a germplasm PUI name in the BMS. | |
Germplasm Origin |
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Germplasm Universal Unique ID (Germplasm UUID or GUUID) | is an alphanumeric string unique across all BMS databases and all BMS instances. It is a BMS database internal and external differentiating identifier. |
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Group Founder | is a germplasm record that has GID equals to Group ID. See grouping. | For Hybrid and Grouped (fixed) lines. |
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Grouping | is an action to set germplasm with a shared ancestry into a group. Grouping is useful when working with genebank accessions, inbred lines, hybrids, clones or varieties of a self-pollinating species for managing highly related or exact materials. | A group is created by selecting a germplasm that is to be the founder of a new group and using the 'Group' action in the Germplasm Manager module. This creates a group identity, a Group ID. When Germplasm with a group identity is propagated using breeding methods that refine or preserve genetic variation (derivative or maintenance methods) the resulting descendants will inherit the group identity. In a typical hybrid breeding program when a line is considered homozygous (fixed), either by inbreeding or doubled haploid formation, it is set as the founder of a new group and given usually a code name. Grouping and coding can also be useful to track families and to indicate when germplasm has passed through a breeding phase, such as disease resistance selections. The primary reason for grouping inbred lines is to declare them fixed - in the sense of having a distinct and relatively stable genotype. For clonally propagated crops, grouping is useful when relevant materials are cloned and the new germplasm records obtain a new GID and maintain its connection to the founder via the Group ID. |
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Group Source, Germplasm | identifies most recent ancestor created by a generative breeding method from which the derivative germplasm was obtained and is simply the GID of the initial germplasm. Also known as root germplasm record or cross of origin. | A germplasm record that is produced through a derivative germplasm creation method or a maintenance germplasm creation method has one immediate source (progenitor), referred to in BMS applications as the plot (seed) source. If we trace back the genealogy of germplasm records produced only through derivative or maintenance germplasm creation methods, we will end up at a germplasm record that either has unknown progenitors (such as a landrace or a breeding line of unknown provenance), or is the product of a generative germplasm creation method. We consider this germplasm record as the root of a derivative neighborhood, known in BMS as the Group Source. |
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Group (Source) Relatives, Germplasm | is a list of all germplasm records that had been obtained by derivation or maintenance steps from the group source (cross of origin). | In the Pedigree tab of the Germplasm detail a user can retrieve the list of germplasm records with in common group source. This query list all germplasm records produced only through derivative or maintenance germplasm creation methods with in common direct group source, thus returning the same list for all its members. |
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Head to Head Query | The head to head query allows a breeder to compare the performance of test germplasm to standard entries across studies for specified trait/s. Breeders can |
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Inventory Attribute, Variable Type | is a BMS variable type used for annotating data at inventory lots. |
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L-O
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Lot, Inventory | A lot is a batch of propagules harvested, or collected together into a single group.
| BMS can manage inventories of seeds, plant cuttings, tissue cultures, pollen, spores, and others propagules where each lot is associated to a Lot ID, Lot UID, Stock ID, Storage Location, Lot attributes, Lot amounts and Lot transactions. It is a good practice to maintain lots as the unique combination of a germplasm (GID) harvested on a certain source location, but if necessary BMS allows users to split or merge lots.
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Lot ID | is a numeric key for inventory lots, created as an incremental sequence by BMS. |
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Lot UID | is the alphanumeric unique identifier for inventory lots, created automatically by BMS. | It is recommended for barcoding inventory lots. |
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Management Neighbors, Germplasm | A management neighborhood is a special kind, and may be a subset, of a maintenance neighborhood. It is a list of all germplasm records that belong to a group linked to a germplasm group founder, its Group ID is the founder GID. See Grouping. | In addition to being in the same maintenance neighborhood, all the germplasm samples in a management neighborhood are under the responsibility [sic; note responsibility NOT necessarily ownership] of a single organization. For example, the stocks of a modern released cultivar maintained by one seed company would form one management neighborhood of the variety’s maintenance neighborhood. |
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Maintenance Breeding Method | Maintenance methods applied to a source progenitor or population (single GID) maintain a specific level of genetic variation with the goal of creating new instances of germplasm as similar to the progenitor as possible, such as a seed increase. |
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Maintenance Neighborhood, Germplasm | All germplasm records produced from a common progenitor record through maintenance germplasm creation methods form a maintenance neighborhood. In a maintenance neighborhood, all germplasm records are produced from one common progenitor with the aim of maintaining the genetic diversity of that common progenitor. | A common example is a modern released cultivar. Breeders and seed companies try to maintain the genetic identity of a cultivar fixed, despite repeated cycles of propagating new samples of the cultivar and distribution to different parts of the target market area. All records of one such variety are linked in a single maintenance neighborhood. (By contrast, a landrace or traditional cultivar is not a maintenance neighborhood: such cultivars have been jointly developed by farmers, often from many communities over many years. Extant records of a single landrace can be genetically distinct and only distantly related, through many generations of hybridization, introgression and selection. Commonly each record of a landrace is heterogeneous and farmers commonly make their own selections each year, as they seek to improve the landrace rather than maintain its identity) | NOT Working…ticket? |
Method, Variable |
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Name Type, Germplasm |
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Non-Standard Selection History | A non-standard selection history is any conglomeration of characters that uniquely identify a particular cross and the selections made from the progeny of the cross. BMS offers limited support for non-standard selection histories. However, non-standard selection histories convey no syntactic or semantic information other than to identify germplasm as being unique. | Some exceptions to the standardization of selection histories are recognized. A plant may be found in the field. Nothing is known about the plant’s pedigree but it is introduced into the breeding program because of one or more exceptional qualities. These plants are assigned an arbitrary but unique cross name and/or selection history. Further selections may be made in subsequent cycles. There are also cases where a named cultivar or breeding line is used in a breeding program but its selection history is not fully known. Such material is assigned a non-standard selection history where the identifying string contains as much information as is known. This may vary from nothing to nearly complete information. Neither the selection history nor the cross name need be unique in themselves. However, the combination of cross name and selection history must be unique. The above case includes introduction material where the pedigree does not conform, and cannot be made to conform, to BMS naming customization. |
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Nursery | is a study type. Usually used for studies with a non replicated layout in a single environment for germplasm development or maintenance purposes. | The most common field layouts for nurseries are simply entry list order, a entry list order with a checks insertion pattern, or more sophisticated like matting designs (parental material arrangement) or augmented designs. BMS may generated some of the mentioned or accept an externally generated experimental design or field layout. | Crossing Nursery Fn Selection Nursery Seed increase Nursery |
Observation Unit | is the unit upon which observations or measurements are made (this may not be the same as the experimental unit). | The BMS manual and documentation will use "plots" to generically describe the highest level of observation, as this is the most common experimental unit in breeding. Levels of measurement (observation) In this section we distinguish among measurements that are taken at three different levels: -Individual plants. A key feature of many genetic resources evaluation trials is that they involve genetically heterogeneous material, i.e. there is variation among the plants in each accession. Hence some data, for example on plant height, will be needed at the “plant level“, i.e. collected on a number of individual plants in each plot, to summarize the information from accessions fully. -Plots. Each germplasm (treatment) is planted on a small piece of land or sometimes in a pot. Some measurements are normally made at this “plot level”, e.g. by recording a single value for the whole plot, as with yield. -The study instance site (environment) as a whole. To interpret the results of a trial it is important to provide details of the environment within which the trial was conducted. Thus, we also collect data at the site or “trial level”, for example site location, date of sowing and rainfall. | A data point or observation is a set of one or more measurements on a single member of the unit of observation. |
Ontology | is a special type of controlled vocabulary that has been formalized into a hierarchical arrangement such that very specific terms (e.g., leaf production, epidermal cell) are categories of more generic terms (e.g., vegetative growth, cell). Furthermore, an ontology describes a hierarchy where any term can have more than one parent term, and where parent-child relationships can be of different types. For example, an epidermal cell is a type of cell, and it is also part of an epidermis which is a type of tissue. An ontology also allows classification of terms that are synonymous: an epidermis is an outer cell layer. |
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P-S
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P-Rep Design | Partially Replicated (P-Rep) experimental designs fully replicate check entries and a proportion of test entries in every study instance - thus permitting a limited inventory of test germplasm to be tested over a larger number of environments. | BMS can generate Partially Replicated (P-Rep) experimental design where test entries are replicated once in the design and check/s entry/ies appear once in each block. |
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Pedigree | is a chain of GIDs linked by breeding methods used to describe ancestry of a germplasm record. This BMS definition of pedigree allows flexibility for missing data and revision. A breeder can revise a breeding method or GID without needing to update naming conventions, pedigree text string, or other genealogical dependencies. See Pedigree Graph and Cross. | BMS reports germplasm pedigrees in two formats, pedigree graph or cross string.
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Pedigree Graph | is a visual visualization of the ancestry of a germplasm record. | The pedigree tree graph is accessible at the Pedigree tab of a Germplasm record, by default is generated with three generative levels, user may adjust the levels and add the derivative and maintenance intermediate levels. Female and male parents are connected with a red and a blue arrow, respectively. For derivative and maintenance connection steps the arrow is black. |
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Permission, Users and Roles | Permissions define the actions that a user can perform in the BMS. |
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PUI | See Germplasm Permanent Unique ID. |
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Plot | is the basic physical unit for studies that receives a particular treatment. (see Experimental Unit) |
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Plot Source/Code (former Seed Source) PLOTCODE_AP_text | is a BMS generated string describing the origin of the Germplasm. It is stored as the Passport Variable PLOTCODE_AP_text in he Germplasm record. See also Germplasm Origin. | The formats consist of placeholders that will be replaced during the generation of the string, along with literal characters that are inserted into the string as they are shown in the configuration file. Some elements of these formats rely on variables being present in the nursery or trial, as detailed below. The default format for Plot Source strings for trials is [NAME]:[LABBR]:[SEASON]:[PLOTNO]:[PLANT_NO]. Contact your BMS administrator for a customized PLOTCODE_AP_text | Given an Study with the following details: Study Name= MyTrial Plot= 3 Plant= 5 |
Preferred Name, Germplasm | is the main or principal chosen name of a germplasm. A germplasm record in BMS can hold multiple names for a single germplasm, if more than one name user must define the preferred name. | It is recommended to establish a convention for preferred name assignation to germplasm records holding multiple names. (e.g. priority follows Variety Name > Line Name > Code 1 > Derivative Name….) |
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Process Code | is a instruction that retrieve and insert information into the name string. Process codes are used for generating germplasm names and plot codes. | Using process codes in the breeding methods table allows BMS users customization of Cross Code and Selection Term used in the derivative name (Selection History) construction. Process Codes available for use in name generation
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Program (Breeding Program) | is the space of a group of BMS users working in a common crop, projects and objectives. A BMS Crop DB can contain multiple programs. A BMS Program can contain multiple Studies. | Crop DB in BMS maintain germplasm records in sync for all programs within the crop. Programs separate studies and project management activities separated one of each other. | Pre-breeding Program, Conventional Breeding Program, Hybrid Breeding Program, Biotech Breeding Program, Special Program |
Property, Variable |
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Randomized Complete Block Design (RCBD) | is a experimental design where each of the v, treatments occurs once in every block (or replicate), and the number of units per block, k, is constant and equal to the number of treatments (v = k). | It may include check entry/ies that are replicated and randomized like the test entries. Treatment factors can be added to RCB for a multifactorial design. |
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Reference, Germplasm | is the identifier of bibliographic reference or note from where the Germplasm data was retrieved. |
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Replicate factor | is how replications are distributed within the experimental layout. Also known as blocking factors. | Replicate or blocking is a non-random arrangement of experimental units into groups (reps or blocks) consisting of units that are similar to one another. Blocking reduces known but irrelevant sources of variation between units and thus allows greater precision in the estimation of the source of variation under study. For most experimental design generated in BMS the replicate factor is described as REP_NO. | Example of a RIBD with 3 non-random replication (REP_NO) and 3 random incomplete blocks (BLOCK_NO) of 5 entries each.
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Replications (Reps) | is the repetition of the experimental treatment. See Replicate factor. | For complete blocks design is the number of experimental units (plots) containing each germplasm entry within the experimental layout. |
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Resolvable Incomplete Block Design (RIBD) | is a experimental design where plots (experimental units) are grouped into blocks that are not large enough to contain all germplasm entries (treatments). | Resolvable blocks are created by grouping incomplete blocks together, so that each treatment is replicated exactly once in each group or set. Number of germplasm cannot be prime. Block size must be greater than 1 and a common denominator of the number of germplasm. It may include check entry/ies that are replicated and randomized like the test entries. Lattice designs are a well known type of resolvable incomplete block design Lattices are special cases of incomplete block designs. Here we just consider square lattices, where the number of accessions is a perfect square, for example 9, 16, 25, 144 or 900. In a square lattice, the block size is fixed as the square root of the number of accessions. So, with 900 accessions the blocks would be of 30 plots each. Thus lattices provide simple designs for situations where there are many accessions and blocks are reasonably small compared with the size of the trial. When blocking turns out to be ineffective, RIBD can be analyzed as an RCBD if designed with 2 or more replications. |
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Role | Roles provide a way for administrators to group permissions and assign them to users. |
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Row-And-Column Design (RowColD) | is a experimental design where treatments (germplasm entries) are distributed on experimental units (plots) considering constraints in two directions. | When the heterogeneity is known or suspected in two directions, rows and columns, Row-and-Column designs can be used to group experimental units in two directions. The purpose of a RowColD is to eliminate equally from the errors all differences among rows and among columns. Under these situations, the experimental material should be arranged and the experiment conducted so that the differences among rows and columns represent major sources of variation. The number of germplasm entries cannot be prime. The number of rows per replication multiplied by the columns per replication must equal the number of germplasm per replication. |
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Sample |
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Sampling Unit |
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Scale, Variable |
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Selection Term | is an identifier of the selection and advance process used in the selection history syntax. | Selection Term= Prefix + Count + Suffix |
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Simple Cross Name | is a cross name that does not contain cross symbols. | Simple cross names are names that are given to land races, breeding lines and cultivars. In general, a simple cross name is a synonym for a composite cross name - selection history combination. It may also be a synonym for a breeding line, that is, a cross and all of its progeny (siblings). |
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STA BrAPP (Decision Support Tool) | is a statistical analysis cloud based App that accompanies the BMS. Developed by….. | STA BrAPP can be launched from BMS Study Manager to run data quality control and analysis of trial experiments using R packages as SpATS and lme4. Currently STA BrAPP is in pre-release (Beta) status, please contact BMS administrator to activate it in your BMS instance. |
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Standard Selection History | A standard selection history conforms to the syntax and semantics rules. | The term "selection history" implies a standard selection history unless stated otherwise. All selection histories generated by BMS will conform to the standard selection history syntax and semantics. A standard selection history may consists of the following items: A Cross code and selection steps identifiers. Each item is separated from the others by a separator, usually hyphen for derivative methods or a colon for maintenance methods. |
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Stock ID | is a readable coded name for the inventory lots. | it may be used for barcoding, but not recommended
| Stock ID = prefix + batch number + separator '-' + sequential lot number in batch SID32-1; SID32-2; SID32-17; SID45-3 |
Study | is the basic, reportable unit of research, a planned and organized inquiry, a nursery for creating new germplasm, a single or multi-environment experiment for observing germplasm performance. It is synonymous with the notions of experiment, nursery, trial or survey. Since the BMS must deal with any of these, we use the term study. The study concept in BMS corresponds to the "investigation" concept in MIAPPE, “experiment” concept in EBS or "trial" concept in BrAPI. | A study is characterized by a set of scientific objectives and testable hypotheses and results in the collection of one or more data sets. The division of data into sets is usually motivated by convenience; for example, data collected from different observation levels are most conveniently treated in different data sets. Similarly, data collected at different times or from different plot areas are also often treated as different data sets, although it is feasible to treat these divisions in a single data set. The point is that the BMS is flexible enough to manage data in all the ways that researchers require. A Study can contain one or multiple Environments (Instances or Occurrences). | A crossing block nursery, a F3 nursery, an observation nursery, a seed increase nursery, a single location trial, a multi-location trial are all examples of BMS studies. |
Study Book | is the table or logbook associated to each study for recording data and notes. The Study Book concept in BMS correspond to the “Field” concept in Fieldbook App. | In general, each Study Book represent a single instance trial or nursery dataset. Dataset may represent Observation (Plot) or Sub-observation (repeated measurement, time series) levels. BMS can generate several electronic Study Book formats: Excel, csv or Fieldbook App format. |
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Study Type | is a class assigned to studies. | By default BMS is deployed with Trial and Nursery study types. By customization other types may be added as: Observational nursery Crossing block International nursery Regulated trial VCU trial Confined field trial |
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Study Settings | Administrative data are collected as part of the day to day processes and record keeping of the breeding program/organization at the level of the BMS studies. |
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Sub-Observation |
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T-Z
Name | Definition | Guidelines | Example |
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Time Series | is a collection of observations of well-defined data items obtained through repeated measurements over time. |
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Trait | The term “trait” is used synonymously with the term “variate” and can refer to anything that is measured or observed (including covariates). | See Trait, Variable Type.
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Trait Dictionary | is a publication reference listing trait variables of a particular crop species, giving information about their meanings and other relevant information. See Trait Variable. | Recommendations for creating and managing TDs: https://hdl.handle.net/10568/110906 | Access current Crop public TDs at Crop Ontology Site |
Trait, Variable Type | is a BMS variable type used for annotating data at observation and/or sub-observations levels. They are commonly known as Response, Dependent or Outcome Variables or Variates. It is called “Trait” in BMS documentation since most cases represent phenotypic measurements in studies. | A trait variable is the combination of 1 trait (property in the Ontology Manager), 1 method and 1 scale. ● A trait: “what is observed” ● A method: “how the observation is made” ● A scale: “how the observation is expressed” | PH_Meas_cm = Plant height by Measuring Method reported in centimeters |
Transaction, Inventory Lot | is a confirmed or pending action on a inventory lot. Inventory reservations, withdrawals, and deposits are recorded as transactions within a lot. |
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Treatment | is the combination of experimental conditions applied to an experimental unit. See Treatment Factor. |
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Treatment Factor, Variable Type | is a BMS variable type that specify treatment factors other than Germplasm to be used in multifactorial experimental design. | For using treatment factors in BMS a pair of related variables must be created in the ontology manager in advance to study creation. The pair of variables must share the property, and the variable type as Treatment factor. ……….. |
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Trial | is a study type. Usually used for studies with a replicated experimental design in one or multiple environments for germplasm phenotypic performance evaluation. |
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User Role | A BMS user may have one or more assigned roles that determine the permissions in the BMS. Each role is limited to one Instance, Crop or Program level. |
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Universal Unique ID (UUID) | is an alphanumeric string unique across all BMS databases and all BMS instances assigned to different objects or entities in database (Germplasm record, Inventory Lot, Observation or Sub-Observation Unit, Sample). It is a BMS database internal and external differentiating identifier. |
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Variable | is any factor, term or condition that can exist in differing amounts or types, they also provide a way of labeling data with a descriptive name. Variables are used to store information to be referenced and manipulated in BMS database. See variable type. | Controlled vocabulary terms |
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Variable Type | is a class assigned to DB controlled vocabulary terms used in BMS. Its main purpose is to specify where and how a variable is used in the BMS. |
| BMS Variable Types: Inventory Analysis Summary Analysis Entry Detail Environment Condition Environment Detail Experimental Design Germplasm Attribute Germplasm Descriptor Germplasm Passport Inventory Attribute Observation Unit Selection Method Study Detail Trait Treatment Factor |