valuesets 0.3.1__py3-none-any.whl

valuesets/schema/bio/insdc_missing_values.yaml

@@ -0,0 +1,85 @@
+name: insdc_missing_values
+id: https://w3id.org/linkml/valuesets/bio/insdc_missing_values
+prefixes:
+  NCIT: http://purl.obolibrary.org/obo/NCIT_
+  OBI: http://purl.obolibrary.org/obo/OBI_
+  IAO: http://purl.obolibrary.org/obo/IAO_
+  SIO: http://semanticscience.org/resource/SIO_
+  insdc: https://www.insdc.org/controlled-vocabulary/missing-value/
+  valuesets: https://w3id.org/valuesets/
+default_prefix: valuesets
+slots:
+  insdc_missing_value:
+    description: INSDC (International Nucleotide Sequence Database Collaboration) controlled vocabulary for missing values
+      in sequence records
+    range: InsdcMissingValueEnum
+enums:
+  InsdcMissingValueEnum:
+    description: INSDC (International Nucleotide Sequence Database Collaboration) controlled vocabulary for missing values
+      in sequence records
+    permissible_values:
+      NOT_APPLICABLE:
+        description: Information is inappropriate to report, can indicate that the standard itself fails to model or represent
+          the information appropriately
+        meaning: NCIT:C48660
+        title: not applicable
+      MISSING:
+        description: Not stated explicitly or implied by any other means
+        meaning: NCIT:C54031
+        title: missing
+      NOT_COLLECTED:
+        description: Information of an expected format was not given because it has never been collected
+        meaning: NCIT:C142610
+        title: Missing Data
+        annotations:
+          note: NCIT:C142610 represents Missing Data which encompasses data not collected
+      NOT_PROVIDED:
+        description: Information of an expected format was not given, a value may be given at the later stage
+        meaning: NCIT:C126101
+        title: Not Available
+        annotations:
+          note: Using NCIT:C126101 (Not Available) as a general term for data not provided
+      RESTRICTED_ACCESS:
+        description: Information exists but cannot be released openly because of privacy concerns
+        meaning: NCIT:C67110
+        title: Data Not Releasable
+        annotations:
+          note: NCIT:C67110 represents Data Not Releasable due to confidentiality
+      MISSING_CONTROL_SAMPLE:
+        description: Information is not applicable to control samples, negative control samples (e.g. blank sample or clear
+          sample)
+        annotations:
+          note: No specific ontology term found for missing control sample data
+      MISSING_SAMPLE_GROUP:
+        description: Information can not be provided for a sample group where a selection of samples is used to represent
+          a species, location or some other attribute/metric
+        annotations:
+          note: No specific ontology term found for missing sample group data
+      MISSING_SYNTHETIC_CONSTRUCT:
+        description: Information does not exist for a synthetic construct
+        annotations:
+          note: No specific ontology term found for missing synthetic construct data
+      MISSING_LAB_STOCK:
+        description: Information is not collected for a lab stock and its cultivation, e.g. stock centers, culture collections,
+          seed banks
+        annotations:
+          note: No specific ontology term found for missing lab stock data
+      MISSING_THIRD_PARTY_DATA:
+        description: Information has not been revealed by another party
+        meaning: NCIT:C67329
+        title: Source Data Not Available
+        annotations:
+          note: NCIT:C67329 represents Source Data Not Available
+      MISSING_DATA_AGREEMENT_ESTABLISHED_PRE_2023:
+        description: Information can not be reported due to a data agreement established before metadata standards were introduced
+          in 2023
+        annotations:
+          note: No specific ontology term for data missing due to pre-2023 agreements
+      MISSING_ENDANGERED_SPECIES:
+        description: Information can not be reported due to endangered species concerns
+        annotations:
+          note: No specific ontology term for data withheld due to endangered species
+      MISSING_HUMAN_IDENTIFIABLE:
+        description: Information can not be reported due to identifiable human data concerns
+        annotations:
+          note: No specific ontology term for data withheld due to human identifiability

valuesets/schema/bio/lipid_categories.yaml

@@ -0,0 +1,72 @@
+name: lipid_categories
+title: Lipid Categories
+description: Major lipid categories from SwissLipids classification
+id: https://w3id.org/valuesets/bio/lipid_categories
+imports:
+- ../core
+prefixes:
+  linkml: https://w3id.org/linkml/
+  SLM: https://swisslipids.org/rdf/SLM_
+  CHEBI: http://purl.obolibrary.org/obo/CHEBI_
+  valuesets: https://w3id.org/valuesets/
+default_prefix: valuesets
+slots:
+  lipid_category:
+    description: Major categories of lipids based on SwissLipids classification
+    range: LipidCategory
+enums:
+  LipidCategory:
+    title: Lipid Category
+    description: Major categories of lipids based on SwissLipids classification
+    permissible_values:
+      LIPID:
+        description: Lipid
+        meaning: CHEBI:18059
+        broad_mappings:
+        - SLM:000389145
+      FATTY_ACYLS_AND_DERIVATIVES:
+        description: Fatty acyls and derivatives
+        meaning: CHEBI:24027
+        aliases:
+        - fatty-acyl group
+        broad_mappings:
+        - SLM:000390054
+      GLYCEROLIPIDS:
+        description: Glycerolipids
+        meaning: CHEBI:35741
+        aliases:
+        - glycerolipid
+        exact_mappings:
+        - SLM:000117142
+      GLYCEROPHOSPHOLIPIDS:
+        description: Glycerophospholipids
+        meaning: CHEBI:37739
+        aliases:
+        - glycerophospholipid
+        exact_mappings:
+        - SLM:000001193
+      SPHINGOLIPIDS:
+        description: Sphingolipids
+        meaning: CHEBI:26739
+        aliases:
+        - sphingolipid
+        exact_mappings:
+        - SLM:000000525
+      STEROIDS_AND_DERIVATIVES:
+        description: Steroids and derivatives
+        meaning: CHEBI:35341
+        aliases:
+        - steroid
+        exact_mappings:
+        - SLM:000500463
+        narrow_mappings:
+        - CHEBI:15889
+      PRENOL_LIPIDS:
+        description: Prenol Lipids
+        meaning: CHEBI:24913
+        aliases:
+        - isoprenoid
+        exact_mappings:
+        - SLM:000508860
+        narrow_mappings:
+        - CHEBI:16019

valuesets/schema/bio/plant_biology.yaml

@@ -0,0 +1,125 @@
+name: plant_biology
+title: Plant Biology Value Sets
+description: 'Value sets related to plant biology, including reproductive systems,
+
+  breeding systems, and other plant-specific characteristics.'
+id: https://w3id.org/linkml/valuesets/bio/plant_biology
+imports:
+- linkml:types
+prefixes:
+  valuesets: https://w3id.org/valuesets/
+  GSSO: http://purl.obolibrary.org/obo/GSSO_
+  PATO: http://purl.obolibrary.org/obo/PATO_
+  PO: http://purl.obolibrary.org/obo/PO_
+  TO: http://purl.obolibrary.org/obo/TO_
+  ECOCORE: http://purl.obolibrary.org/obo/ECOCORE_
+default_prefix: valuesets
+slots:
+  plant_sexual_system:
+    description: Sexual systems in plants, describing the distribution and types of reproductive organs (flowers) within and
+      among individual plants
+    range: PlantSexualSystem
+enums:
+  PlantSexualSystem:
+    description: 'Sexual systems in plants, describing the distribution and types of
+
+      reproductive organs (flowers) within and among individual plants.'
+    permissible_values:
+      ANDRODIOECIOUS:
+        text: ANDRODIOECIOUS
+        meaning: GSSO:011874
+        description: A sexual system in which males and hermaphrodites coexist in a population
+      ANDROECIOUS:
+        text: ANDROECIOUS
+        description: Having only male flowers (staminate flowers)
+      ANDROGYNOMONOECIOUS:
+        text: ANDROGYNOMONOECIOUS
+        description: Having male, female, and bisexual flowers on the same plant
+      ANDROGYNOUS:
+        text: ANDROGYNOUS
+        description: Having both male and female reproductive organs; hermaphroditic
+      ANDROMONOECIOUS:
+        text: ANDROMONOECIOUS
+        meaning: GSSO:011870
+        description: Having both male and hermaphroditic flowers on the same plant
+      BISEXUAL:
+        text: BISEXUAL
+        description: Having both male and female reproductive organs in the same flower
+      DICHOGAMOUS:
+        text: DICHOGAMOUS
+        description: Having male and female organs that mature at different times
+      DICLINOUS:
+        text: DICLINOUS
+        description: Having unisexual flowers (either male or female, not both)
+      DIOECIOUS:
+        text: DIOECIOUS
+        meaning: GSSO:011872
+        description: Having male and female flowers on separate plants
+      GYNODIOECIOUS:
+        text: GYNODIOECIOUS
+        meaning: GSSO:011873
+        description: Having female and hermaphroditic plants in the same population
+      GYNOECIOUS:
+        text: GYNOECIOUS
+        description: Having only female flowers (pistillate flowers)
+      GYNOMONOECIOUS:
+        text: GYNOMONOECIOUS
+        meaning: GSSO:011869
+        description: Having both female and hermaphroditic flowers on the same plant
+      HERMAPHRODITIC:
+        text: HERMAPHRODITIC
+        description: Having both male and female reproductive organs
+        meaning: PATO:0001340
+        title: hermaphrodite
+      IMPERFECT:
+        text: IMPERFECT
+        description: Flowers lacking either stamens or pistils (unisexual)
+      MONOCLINOUS:
+        text: MONOCLINOUS
+        description: Having bisexual flowers (both male and female organs)
+      MONOECIOUS:
+        text: MONOECIOUS
+        meaning: GSSO:011868
+        description: Having separate male and female flowers on the same plant
+      PERFECT:
+        text: PERFECT
+        description: Flowers having both stamens and pistils (bisexual)
+      POLYGAMODIOECIOUS:
+        text: POLYGAMODIOECIOUS
+        description: Having male, female, and bisexual flowers on separate plants
+      POLYGAMOMONOECIOUS:
+        text: POLYGAMOMONOECIOUS
+        description: Having male, female, and bisexual flowers on the same plant
+      POLYGAMOUS:
+        text: POLYGAMOUS
+        description: Having male, female, and bisexual flowers
+      PROTANDROUS:
+        text: PROTANDROUS
+        meaning: PATO:0040053
+        description: Starting as male and changing to female at a later stage
+      PROTOGYNOUS:
+        text: PROTOGYNOUS
+        meaning: PATO:0040052
+        description: Starting as female and changing to male at a later stage
+      SUBANDROECIOUS:
+        text: SUBANDROECIOUS
+        description: Predominantly male plants with occasional hermaphroditic flowers
+      SUBDIOECIOUS:
+        text: SUBDIOECIOUS
+        description: Predominantly dioecious with occasional hermaphroditic individuals
+      SUBGYNOECIOUS:
+        text: SUBGYNOECIOUS
+        description: Predominantly female plants with occasional hermaphroditic flowers
+      SYNOECIOUS:
+        text: SYNOECIOUS
+        description: Having male and female organs in the same structure
+      TRIMONOECIOUS:
+        text: TRIMONOECIOUS
+        description: Having male, female, and bisexual flowers on the same plant
+      TRIOECIOUS:
+        text: TRIOECIOUS
+        meaning: GSSO:011875
+        description: Having males, females, and hermaphrodites in the same population
+      UNISEXUAL:
+        text: UNISEXUAL
+        description: Having only one sex (either male or female reproductive organs)

valuesets/schema/bio/plant_developmental_stages.yaml

@@ -0,0 +1,77 @@
+name: plant_developmental_stages
+title: Plant Developmental Stages Value Sets
+description: Value sets for plant developmental stages from germination through senescence
+id: https://w3id.org/common-value-sets/plant_developmental_stages
+imports:
+- linkml:types
+prefixes:
+  CVS: https://w3id.org/common-value-sets/
+  linkml: https://w3id.org/linkml/
+  PO: http://purl.obolibrary.org/obo/PO_
+  valuesets: https://w3id.org/valuesets/
+default_prefix: valuesets
+slots:
+  plant_developmental_stage:
+    description: Major developmental stages in the plant life cycle, from seed germination through senescence
+    range: PlantDevelopmentalStage
+enums:
+  PlantDevelopmentalStage:
+    description: Major developmental stages in the plant life cycle, from seed germination through senescence. Based on the
+      Plant Ontology (PO) standardized stages.
+    permissible_values:
+      SEED_GERMINATION_STAGE:
+        description: Stage beginning with seed imbibition and ending with radicle emergence
+        meaning: PO:0007057
+      SEEDLING_STAGE:
+        description: Stage from germination until development of first adult vascular leaf
+        meaning: PO:0007131
+        aliases:
+        - seedling development stage
+      VEGETATIVE_GROWTH_STAGE:
+        description: Stage of growth before reproductive structure formation
+        meaning: PO:0007134
+        aliases:
+        - sporophyte vegetative stage
+      FLOWERING_STAGE:
+        description: Stage when flowers open with pollen release and/or receptive stigma
+        meaning: PO:0007616
+      FRUIT_DEVELOPMENT_STAGE:
+        description: Stage of fruit formation through ripening
+        meaning: PO:0001002
+      SEED_DEVELOPMENT_STAGE:
+        description: Stage from fertilization to mature seed
+        meaning: PO:0001170
+      SENESCENCE_STAGE:
+        description: Stage of aging with loss of function and organ deterioration
+        meaning: PO:0007017
+        aliases:
+        - sporophyte senescent stage
+      DORMANCY_STAGE:
+        description: Stage of suspended physiological activity and growth
+        meaning: PO:0007132
+        aliases:
+        - sporophyte dormant stage
+      EMBRYO_DEVELOPMENT_STAGE:
+        description: Stage from zygote first division to seed germination initiation
+        meaning: PO:0007631
+        aliases:
+        - plant embryo development stage
+      ROOT_DEVELOPMENT_STAGE:
+        description: Stages in root growth and development
+        meaning: PO:0007520
+      LEAF_DEVELOPMENT_STAGE:
+        description: Stages in leaf formation and expansion
+        meaning: PO:0001050
+      REPRODUCTIVE_STAGE:
+        description: Stage from reproductive structure initiation to senescence onset
+        meaning: PO:0007130
+        aliases:
+        - sporophyte reproductive stage
+      MATURITY_STAGE:
+        description: Stage when plant or plant embryo reaches full development
+        meaning: PO:0001081
+        aliases:
+        - mature plant embryo stage
+      POST_HARVEST_STAGE:
+        description: Stage after harvest when plant parts are detached from parent plant
+default_range: string

valuesets/schema/bio/plant_sex.yaml

@@ -0,0 +1,108 @@
+name: plant_sex
+id: https://w3id.org/linkml/valuesets/bio/plant_sex
+prefixes:
+  GSSO: http://purl.obolibrary.org/obo/GSSO_
+  PATO: http://purl.obolibrary.org/obo/PATO_
+  UBERON: http://purl.obolibrary.org/obo/UBERON_
+  ECOCORE: http://purl.obolibrary.org/obo/ECOCORE_
+  mixs: https://genomicsstandardsconsortium.github.io/mixs/
+  valuesets: https://w3id.org/valuesets/
+default_prefix: valuesets
+slots:
+  plant_sex:
+    description: Plant reproductive and sexual system types
+    range: PlantSexEnum
+enums:
+  PlantSexEnum:
+    description: Plant reproductive and sexual system types
+    permissible_values:
+      ANDRODIOECIOUS:
+        description: Having male and hermaphrodite flowers on separate plants
+        title: Androdioecious
+      ANDROECIOUS:
+        description: Having only male flowers
+        title: Androecious
+      ANDROGYNOMONOECIOUS:
+        description: Having male, female, and hermaphrodite flowers on the same plant
+        title: Androgynomonoecious
+      ANDROGYNOUS:
+        description: Having both male and female reproductive organs in the same flower
+        title: Androgynous
+      ANDROMONOECIOUS:
+        description: Having male and hermaphrodite flowers on the same plant
+        title: Andromonoecious
+      BISEXUAL:
+        description: Having both male and female reproductive organs
+        title: Bisexual
+      DICHOGAMOUS:
+        description: Male and female organs mature at different times
+        title: Dichogamous
+      DICLINOUS:
+        description: Having male and female reproductive organs in separate flowers
+        title: Diclinous
+      DIOECIOUS:
+        description: Having male and female flowers on separate plants
+        meaning: GSSO:011872
+        title: Dioecious
+      GYNODIOECIOUS:
+        description: Having female and hermaphrodite flowers on separate plants
+        title: Gynodioecious
+      GYNOECIOUS:
+        description: Having only female flowers
+        title: Gynoecious
+      GYNOMONOECIOUS:
+        description: Having female and hermaphrodite flowers on the same plant
+        title: Gynomonoecious
+      HERMAPHRODITIC:
+        description: Having both male and female reproductive organs
+        meaning: UBERON:0007197
+        title: hermaphroditic organism
+      IMPERFECT:
+        description: Flower lacking either male or female reproductive organs
+        title: Imperfect
+      MONOCLINOUS:
+        description: Having both male and female reproductive organs in the same flower
+        title: Monoclinous
+      MONOECIOUS:
+        description: Having male and female flowers on the same plant
+        meaning: GSSO:011868
+        title: Monoecious
+      PERFECT:
+        description: Flower having both male and female reproductive organs
+        title: Perfect
+      POLYGAMODIOECIOUS:
+        description: Having male, female, and hermaphrodite flowers on separate plants
+        title: Polygamodioecious
+      POLYGAMOMONOECIOUS:
+        description: Having male, female, and hermaphrodite flowers on the same plant
+        title: Polygamomonoecious
+      POLYGAMOUS:
+        description: Having male, female, and hermaphrodite flowers
+        title: Polygamous
+      PROTANDROUS:
+        description: Male organs mature before female organs
+        title: Protandrous
+      PROTOGYNOUS:
+        description: Female organs mature before male organs
+        title: Protogynous
+      SUBANDROECIOUS:
+        description: Mostly male flowers with occasional hermaphrodite flowers
+        title: Subandroecious
+      SUBDIOECIOUS:
+        description: Mostly dioecious with occasional hermaphrodite flowers
+        title: Subdioecious
+      SUBGYNOECIOUS:
+        description: Mostly female flowers with occasional hermaphrodite flowers
+        title: Subgynoecious
+      SYNOECIOUS:
+        description: Having male and female organs fused together
+        title: Synoecious
+      TRIMONOECIOUS:
+        description: Having male, female, and hermaphrodite flowers on the same plant
+        title: Trimonoecious
+      TRIOECIOUS:
+        description: Having male, female, and hermaphrodite flowers on separate plants
+        title: Trioecious
+      UNISEXUAL:
+        description: Having only one sex of reproductive organs
+        title: Unisexual

valuesets/schema/bio/protein_evidence.yaml

@@ -0,0 +1,63 @@
+name: protein_evidence
+title: Protein Evidence Value Sets
+description: Value sets related to protein evidence and annotation status
+id: https://w3id.org/common-value-sets/protein_evidence
+imports:
+- linkml:types
+prefixes:
+  CVS: https://w3id.org/common-value-sets/
+  linkml: https://w3id.org/linkml/
+  valuesets: https://w3id.org/valuesets/
+default_prefix: valuesets
+slots:
+  protein_evidence_for_existence:
+    description: The evidence for the existence of a biological entity
+    range: ProteinEvidenceForExistence
+  ref_seq_status:
+    description: RefSeq status codes, taken from https://www
+    range: RefSeqStatusType
+enums:
+  ProteinEvidenceForExistence:
+    description: The evidence for the existence of a biological entity. See https://www.uniprot.org/help/protein_existence
+      and https://www.ncbi.nlm.nih.gov/genbank/evidence/.
+    permissible_values:
+      EXPERIMENTAL_EVIDENCE_AT_PROTEIN_LEVEL:
+        description: Indicates that there is clear experimental evidence for the existence of the protein. The criteria include
+          partial or complete Edman sequencing, clear identification by mass spectrometry, X-ray or NMR structure, good quality
+          protein-protein interaction or detection of the protein by antibodies.
+      EXPERIMENTAL_EVIDENCE_AT_TRANSCRIPT_LEVEL:
+        description: Indicates that the existence of a protein has not been strictly proven but that expression data (such
+          as existence of cDNA(s), RT-PCR or Northern blots) indicate the existence of a transcript.
+      PROTEIN_INFERRED_BY_HOMOLOGY:
+        description: Indicates that the existence of a protein is probable because clear orthologs exist in closely related
+          species.
+      PROTEIN_PREDICTED:
+        description: Used for entries without evidence at protein, transcript, or homology levels.
+      PROTEIN_UNCERTAIN:
+        description: Indicates that the existence of the protein is unsure.
+  RefSeqStatusType:
+    description: RefSeq status codes, taken from https://www.ncbi.nlm.nih.gov/genbank/evidence/.
+    permissible_values:
+      MODEL:
+        description: The RefSeq record is provided by the NCBI Genome Annotation pipeline and is not subject to individual
+          review or revision between annotation runs.
+      INFERRED:
+        description: The RefSeq record has been predicted by genome sequence analysis, but it is not yet supported by experimental
+          evidence. The record may be partially supported by homology data.
+      PREDICTED:
+        description: The RefSeq record has not yet been subject to individual review, and some aspect of the RefSeq record
+          is predicted.
+      PROVISIONAL:
+        description: The RefSeq record has not yet been subject to individual review. The initial sequence-to-gene association
+          has been established by outside collaborators or NCBI staff.
+      REVIEWED:
+        description: The RefSeq record has been reviewed by NCBI staff or by a collaborator. The NCBI review process includes
+          assessing available sequence data and the literature. Some RefSeq records may incorporate expanded sequence and
+          annotation information.
+      VALIDATED:
+        description: The RefSeq record has undergone an initial review to provide the preferred sequence standard. The record
+          has not yet been subject to final review at which time additional functional information may be provided.
+      WGS:
+        description: The RefSeq record is provided to represent a collection of whole genome shotgun sequences. These records
+          are not subject to individual review or revisions between genome updates.
+default_range: string

valuesets/schema/bio/proteomics_standards.yaml

@@ -0,0 +1,116 @@
+name: proteomics_standards
+title: Proteomics Standards
+description: Controlled vocabularies for mass spectrometry and proteomics data annotation from HUPO-PSI standards
+id: https://w3id.org/common-value-sets/bio/proteomics_standards
+imports:
+- linkml:types
+- ../core
+prefixes:
+  linkml: https://w3id.org/linkml/
+  MS: http://purl.obolibrary.org/obo/MS_
+  PRIDE: http://purl.obolibrary.org/obo/PRIDE_
+  UO: http://purl.obolibrary.org/obo/UO_
+  cvs: https://w3id.org/common-value-sets/
+  valuesets: https://w3id.org/valuesets/
+default_prefix: valuesets
+slots:
+  peak_annotation_series_label:
+    description: Types of peak annotations in mass spectrometry data
+    range: PeakAnnotationSeriesLabel
+  peptide_ion_series:
+    description: Types of peptide fragment ion series in mass spectrometry
+    range: PeptideIonSeries
+  mass_error_unit:
+    description: Units for expressing mass error in mass spectrometry
+    range: MassErrorUnit
+enums:
+  PeakAnnotationSeriesLabel:
+    title: Peak Annotation Series Label
+    description: Types of peak annotations in mass spectrometry data
+    permissible_values:
+      PEPTIDE:
+        description: Peptide fragment ion
+        exact_mappings:
+        - PRIDE:0000187
+      INTERNAL:
+        description: Internal fragment ion
+      PRECURSOR:
+        description: Precursor ion
+        exact_mappings:
+        - PRIDE:0000263
+        - MS:1001523
+      IMMONIUM:
+        description: Immonium ion
+        exact_mappings:
+        - PRIDE:0000239
+        - MS:1001239
+      REFERENCE:
+        description: Reference peak or calibrant
+      NAMED_COMPOUND:
+        description: Named chemical compound
+      FORMULA:
+        description: Chemical formula
+      SMILES:
+        description: SMILES structure notation
+      UNANNOTATED:
+        description: Unannotated peak
+  PeptideIonSeries:
+    title: Peptide Ion Series
+    description: Types of peptide fragment ion series in mass spectrometry
+    permissible_values:
+      B:
+        description: B ion series - N-terminal fragment with CO
+        exact_mappings:
+        - PRIDE:0000194
+      Y:
+        description: Y ion series - C-terminal fragment with H
+        exact_mappings:
+        - PRIDE:0000193
+        - MS:1001220
+      A:
+        description: A ion series - N-terminal fragment minus CO
+        exact_mappings:
+        - PRIDE:0000233
+      X:
+        description: X ion series - C-terminal fragment plus CO
+        exact_mappings:
+        - PRIDE:0000227
+      C:
+        description: C ion series - N-terminal fragment with NH3
+        exact_mappings:
+        - PRIDE:0000236
+      Z:
+        description: Z ion series - C-terminal fragment minus NH
+        exact_mappings:
+        - PRIDE:0000230
+        - MS:1001230
+      D:
+        description: D ion series - partial side chain cleavage
+      V:
+        description: V ion series - side chain loss from y ion
+      W:
+        description: W ion series - side chain loss from z ion
+      DA:
+        description: DA ion series - a ion with side chain loss
+      DB:
+        description: DB ion series - b ion with side chain loss
+      WA:
+        description: WA ion series - a ion with tryptophan side chain loss
+      WB:
+        description: WB ion series - b ion with tryptophan side chain loss
+  MassErrorUnit:
+    title: Mass Error Unit
+    description: Units for expressing mass error in mass spectrometry
+    permissible_values:
+      PPM:
+        description: Parts per million - relative mass error
+        exact_mappings:
+        - UO:0000169
+      DA:
+        description: Dalton - absolute mass error
+        aliases:
+        - Dalton
+        - u
+        - amu
+        exact_mappings:
+        - UO:0000221