diff --git a/CHANGES.md b/CHANGES.md
index 1af168c..95438d9 100644
--- a/CHANGES.md
+++ b/CHANGES.md
@@ -1,23 +1,59 @@
# Change-log
-## 0.1.0
- - Initial version
+## 0.4.11 (unreleased)
+ - Add generated schema for WS256
+ - Ability to specify max-count and max-text for log partitioning via
+ a command line option to the `import-logs` command.
+ - Use composite lein profiles.
-## 0.2.0
- - Re-organised project structure.
- - Separation of components into separate repositories.
- - Added basic unit test structure.
- - Removed dependency on perl for sorting EDN files.
- - Fixed minor issues with command line interface.
-## 0.3.0
- - Fix error with old-namespace:
- `acetyl` is no longer used, and has been in-lined into the
- pseudoace package.
+## 0.4.10 (2016-07-22)
+ - Bump version of various packages, notably datomic-pro and dynamodb
+ aws-sdk libraries.
+ - Explicitly pass the annotated models filename as arguments to the CLI
+ (Annotated ACeDB models file now lives in the wormbase-pipeline repository).
-## 0.3.1
- - Added ability to generate a report for comparing a dump of classes to values
- against those stored in the database.
+## 0.4.9 - (2016-07-07)
+ - When dumping .ace files, only present the leaf tag (as the `tace`
+ `Show` command) - enables easier comparisons of ace output.
+ - Add functions for dumping a query to .ace files
+
+## 0.4.8 - (2016-06-24)
+ - Fix wrong exit-code when helper.gz is encountered in `sort-edn-log.sh`.
+
+## 0.4.7 - (2016-06-20)
+ - `2_point_data` ACeDB class renamed to two-point-data in annotated
+ models (#33).
+ - Fix for circular xrefs for `phenotype` and
+ `phenotype_not_observed` in annotated models (#46)
+ - Bug in sort-edn-log.sh - Sort command now uses the temporary sort
+ directory.
+
+## 0.4.6 - (2016-06-15)
+ - Added back missing `xbin` function in `pseudoace.binning`.
+
+## 0.4.5 - (2016-06-14)
+ - Remove hard-dependency on datomic-pro.
+ Library users will now have to choose which flavour (and version)
+ of datomic to include.
+ - Made all functions in the `pseudoace.binning` module public.
+ - EDN log sorting script now allows parallel execution.
+ - Annotated models for WS255 (including generated EDN schema)
+
+## 0.4.4 - (2016-05-12)
+ - Support distributing a release bundle using either datomic-free or datomic-pro.
+ - Add generated schema for WS253, WS254
+ - Various minor fixes for the command line interface.
+
+## 0.4.3 - (2016-04-28)
+ - Rollback version of aws library.
+
+## 0.4.2 - (2016-04-28)
+ - Updated documentation.
+
+## 0.4.1 - (2016-04-28)
+ - Use `lein release` for releases.
+ - Bump versions of datomic and storage dependencies.
## 0.4 - (2016-04-25)
- Moved sorting of logs files back out to the shell.
@@ -37,50 +73,21 @@
- Report now generates two files per class when non-zero missing and
added counts are encountered for easy diffing of object names.
-## 0.4.1 - (2016-04-28)
- - Use `lein release` for releases.
- - Bump versions of datomic and storage dependencies.
-
-## 0.4.2 - (2016-04-28)
- - Updated documentation.
-
-## 0.4.3 - (2016-04-28)
- - Rollback version of aws library.
-
-## 0.4.4 - (2016-05-12)
- - Support distributing a release bundle using either datomic-free or datomic-pro.
- - Add generated schema for WS253, WS254
- - Various minor fixes for the command line interface.
-
-## 0.4.5 - (2016-06-14)
- - Remove hard-dependency on datomic-pro.
- Library users will now have to choose which flavour (and version)
- of datomic to include.
- - Made all functions in the `pseudoace.binning` module public.
- - EDN log sorting script now allows parallel execution.
- - Annotated models for WS255 (including generated EDN schema)
-
-## 0.4.6 - (2016-06-15)
- - Added back missing `xbin` function in `pseudoace.binning`.
-
-## 0.4.7 - (2016-06-20)
- - `2_point_data` ACeDB class renamed to two-point-data in annotated
- models (#33).
- - Fix for circular xrefs for `phenotype` and
- `phenotype_not_observed` in annotated models (#46)
- - Bug in sort-edn-log.sh - Sort command now uses the temporary sort
- directory.
+## 0.3.1
+ - Added ability to generate a report for comparing a dump of classes to values
+ against those stored in the database.
-## 0.4.8 - (2016-06-24)
- - Fix wrong exit-code when helper.gz is encountered in `sort-edn-log.sh`.
+## 0.3.0
+ - Fix error with old-namespace:
+ `acetyl` is no longer used, and has been in-lined into the
+ pseudoace package.
-## 0.4.9 - (2016-07-07)
- - When dumping .ace files, only present the leaf tag (as the `tace`
- `Show` command) - enables easier comparisons of ace output.
- - Add functions for dumping a query to .ace files
+## 0.2.0
+ - Re-organised project structure.
+ - Separation of components into separate repositories.
+ - Added basic unit test structure.
+ - Removed dependency on perl for sorting EDN files.
+ - Fixed minor issues with command line interface.
-## 0.4.10 (2016-07-22)
- - Bump version of various packages, notably datomic-pro and dynamodb
- aws-sdk libraries.
- - Explicitly pass the annotated models filename as arguments to the CLI
- (Annotated ACeDB models file now lives in the wormbase-pipeline repository).
+## 0.1.0
+ - Initial version
diff --git a/README.md b/README.md
index 7e0a350..ca7c4ee 100755
--- a/README.md
+++ b/README.md
@@ -172,7 +172,7 @@ This process re-uses the [leiningen deployment tools][12]:
#
# LEIN_PROFILE can be any named lein profile (or multiple delimiter by comma),
# examples:
-# LEIN_PROFILE="aws"
+# LEIN_PROFILE="ddb"
# LEIN_PROFILE="mysql"
# LEIN_PROFILE="postgresql"
# LEIN_PROFILE="dev
diff --git a/generated-schemas/schema256.edn b/generated-schemas/schema256.edn
new file mode 100644
index 0000000..2226d43
--- /dev/null
+++ b/generated-schemas/schema256.edn
@@ -0,0 +1,4134 @@
+(schema
+ db.sys
+ (fields
+ [partiallyIndexed
+ :boolean
+ "System-assigned attribute set to true for transactions not fully incorporated into the index"]
+ [reId
+ :ref
+ "System-assigned attribute for an id e in the log that has been changed to id v in the index"]))
+
+(schema
+ db
+ (fields
+ [ident
+ :keyword
+ :unique-identity
+ "Attribute used to uniquely name an entity."]
+ [excise :enum [:before :beforeT :attrs]]
+ [valueType
+ :ref
+ "Property of an attribute that specifies the attribute's value type. Built-in value types include, :db.type/keyword, :db.type/string, :db.type/ref, :db.type/instant, :db.type/long, :db.type/bigdec, :db.type/boolean, :db.type/float, :db.type/uuid, :db.type/double, :db.type/bigint, :db.type/uri."]
+ [cardinality
+ :enum
+ [:one :many]
+ "Property of an attribute. Two possible values: :db.cardinality/one for single-valued attributes, and :db.cardinality/many for many-valued attributes. Defaults to :db.cardinality/one."]
+ [unique
+ :enum
+ [:identity :value]
+ "Property of an attribute. If value is :db.unique/value, then attribute value is unique to each entity. Attempts to insert a duplicate value for a temporary entity id will fail. If value is :db.unique/identity, then attribute value is unique, and upsert is enabled. Attempting to insert a duplicate value for a temporary entity id will cause all attributes associated with that temporary id to be merged with the entity already in the database. Defaults to nil."]
+ [isComponent
+ :boolean
+ "Property of attribute whose vtype is :db.type/ref. If true, then the attribute is a component of the entity referencing it. When you query for an entire entity, components are fetched automatically. Defaults to nil."]
+ [index
+ :boolean
+ "Property of an attribute. If true, create an AVET index for the attribute. Defaults to false."]
+ [noHistory
+ :boolean
+ "Property of an attribute. If true, past values of the attribute are not retained after indexing. Defaults to false."]
+ [lang
+ :enum
+ [:java :clojure]
+ "Attribute of a data function. Value is a keyword naming the implementation language of the function. Legal values are :db.lang/java and :db.lang/clojure"]
+ [code
+ :string
+ :fulltext
+ "String-valued attribute of a data function that contains the function's source code."]
+ [txInstant
+ :instant
+ :indexed
+ "Attribute whose value is a :db.type/instant. A :db/txInstant is recorded automatically with every transaction."]
+ [fulltext
+ :boolean
+ "Property of an attribute. If true, create a fulltext search index for the attribute. Defaults to false."]
+ [fn
+ :fn
+ "A function-valued attribute for direct use by transactions and queries."]
+ [doc :string :fulltext "Documentation string for an entity."]))
+
+(schema
+ db.install
+ (fields
+ [partition
+ :ref
+ :many
+ "System attribute with type :db.type/ref. Asserting this attribute on :db.part/db with value v will install v as a partition."]
+ [valueType
+ :ref
+ :many
+ "System attribute with type :db.type/ref. Asserting this attribute on :db.part/db with value v will install v as a value type."]
+ [attribute
+ :ref
+ :many
+ "System attribute with type :db.type/ref. Asserting this attribute on :db.part/db with value v will install v as an attribute."]
+ [function
+ :ref
+ :many
+ "System attribute with type :db.type/ref. Asserting this attribute on :db.part/db with value v will install v as a data function."]))
+
+(schema
+ db.excise
+ (fields [attrs :ref :many] [beforeT :long] [before :instant]))
+
+(schema
+ db.alter
+ (fields
+ [attribute
+ :ref
+ :many
+ "System attribute with type :db.type/ref. Asserting this attribute on :db.part/db with value v will alter the definition of existing attribute v."]))
+
+(schema
+ fressian
+ (fields
+ [tag
+ :keyword
+ :indexed
+ "Keyword-valued attribute of a value type that specifies the underlying fressian type used for serialization."]))
+
+(schema
+ pace
+ (fields
+ [identifies-class
+ :string
+ :unique-identity
+ "Attribute of object-identifers (e.g. :gene/id), indicating the name of the corresponding ACeDB class."]
+ [is-hash
+ :boolean
+ "Marks an object-identifier as identifying a hash-model."]
+ [prefer-part
+ :ref
+ "Attribute of object-identifiers indicating a preferred Datomic partition for storing entities of this type."]
+ [tags
+ :string
+ "Space-separated sequence of tag names from the ACeDB model."]
+ [obj-ref
+ :ref
+ "The object-identifier for the type of object referenced by this attribute."]
+ [order
+ :long
+ "The order of positional parameters within a component."]
+ [use-ns
+ :string
+ :many
+ "For a component attribute, specifies that the component entity may contain attributes from the specied namespace (e.g. \"evidence\")."]
+ [fill-default
+ :boolean
+ "Hint that the importer should supply a default value if none is specified in ACeDB."]
+ [xref
+ :ref
+ :many
+ :component
+ "Information about XREFs to this attribute from other classes."]))
+
+(schema
+ pace.xref
+ (fields
+ [tags :string "The XREF's tag-path within this class."]
+ [attribute
+ :ref
+ :unique-identity
+ "The attribute from the foreign class corresponding to this XREF."]
+ [obj-ref
+ :ref
+ "Identity attribute for the object at the outbound end of the XREF."]
+ [import
+ :boolean
+ "Whether inbound occurrences of this XREF be considered by the ACeDB importer."]
+ [export
+ :boolean
+ "Whether inbound occurrences of this XREF be dumped by the .ace file exporter."]
+ [view
+ :boolean
+ "Should inbound occurrences of this XREFbe shown in user-oriented viewers."]
+ [use-ns
+ :string
+ :many
+ "For 'complex' XREFs, a set of namespaces for additional data which should be visible on the inbound end."]))
+
+(schema
+ longtext
+ (fields
+ [id :string :unique-identity "Built-in ?LongText class."]
+ [text
+ :string
+ :fulltext
+ "The text associated with this object.A full-text index will be built."]))
+
+(schema
+ dna
+ (fields
+ [id :string :unique-identity "Built-in ?DNA class."]
+ [sequence :string "The sequence of this DNA."]))
+
+(schema
+ peptide
+ (fields
+ [id :string :unique-identity "Built-in ?Peptide type."]
+ [sequence :string "The sequence of this protein/peptide."]))
+
+(schema
+ importer
+ (fields
+ [temp
+ :string
+ :unique-identity
+ "Identifier used as scaffolding by the timestamp-aware importer. Should generally be excised after import is complete."]
+ [ts-name :string "Username from a legacy timestamp."]))
+
+(schema
+ ordered
+ (fields
+ [id :string :unique-identity]
+ [index :long "Index in an ordered collection."]))
+
+(schema
+ position-matrix
+ (fields
+ [background :ref :component]
+ [values :ref :many :component]
+ [id :string :unique-identity]
+ [description :ref :many :component]
+ [brief-id :string :indexed]
+ [type :enum [:weight :frequency]]
+ [threshold :double :many]
+ [consensus :ref :many :component]
+ [sites-used :long]
+ [derived-from-matrix :ref :many]
+ [bound-by-gene-product :ref :many :component]
+ [transcription-factor :ref :many :component]
+ [remark :ref :many :component]))
+
+(schema
+ position-matrix.value
+ (fields [a :float] [c :float] [g :float] [t :float]))
+
+(schema
+ locatable
+ (fields
+ [score :float "Feature score, as used in ?Feature_data."]
+ [min
+ :long
+ :indexed
+ "The lower bound of a half-open (UCSC-style) interval defining the location."]
+ [method
+ :ref
+ "Method entity defining the meaning of this feature. Required for lightweight features."]
+ [parent
+ :ref
+ "An entity (e.g. sequence or protein) which defines the coordinate system for this locatable."]
+ [max
+ :long
+ :indexed
+ "The upper bound of a half-open (UCSC-style) interval defining the location."]
+ [note
+ :string
+ :many
+ "Human-readable note associated with a lightweight feature."]
+ [murmur-bin
+ :long
+ :indexed
+ "Bottom 20 bits contain a UCSC/BAM-style bin number.High bits contain a Murmur3 hash code for the parent sequence. Only used for locatables attached to a parent with a :sequence/id."]
+ [assembly-parent :ref "The parent sequence in a genome assembly."]
+ [strand
+ :enum
+ [:negative :positive]
+ "Token designating the strand or orientation of this feature. Omit if unknown or irrelevant."]))
+
+(schema
+ splice-confirm
+ (fields
+ [false-splice
+ :ref
+ "sequence entity providing evidence for a false splice site call."]
+ [rnaseq
+ :ref
+ :component
+ "Details of RNA-seq data supporting this intron (uses splice-confirm.rna namespace)."]
+ [cdna :ref "cdna entity which supports this intron."]
+ [ost :ref "sequence entity of an OST which supports this intron."]
+ [utr :ref "sequence entity of a UTR which supports this intron."]
+ [rst :ref "sequence entity of an RST which supports this intron."]
+ [mass-spec
+ :ref
+ "mass-spec-peptide entity which supports this intron."]
+ [homology
+ :string
+ "accession number of an external database record which supports this intron (is this used?)."]
+ [mrna :ref "sequence entity of an mRNA which supports this intron."]
+ [inconsistent
+ :ref
+ "sequence entity providing evidence for an inconsistent splice site call."]
+ [est :ref "sequence entity of an EST which supports this intron."]))
+
+(schema
+ splice-confirm.rnaseq
+ (fields
+ [analysis :ref "Analysis entity describing the RNA-seq dataset."]
+ [count :long "Number of reads supporting the intron."]))
+
+(schema
+ homology
+ (fields
+ [min
+ :long
+ :indexed
+ "Lower bound of a half-open interval defining the extent of this homology in the target's coordinate system."]
+ [gap
+ :string
+ "Gapped alignment. The locations of matches and gaps are encoded in a CIGAR-like format as defined in http://www.sequenceontology.org/gff3.shtml"]
+ [expr
+ :ref
+ "Expression-pattern which is mapped to a sequence by this homology."]
+ [target-species :ref "Link to target species of alignment."]
+ [dna
+ :ref
+ "Sequence entity representing the target of a DNA homology."]
+ [structure
+ :ref
+ "Structure-data which is mapped to a sequence by this homology."]
+ [max
+ :long
+ :indexed
+ "Upper bound of a half-open interval defining the extent of this homology in the target's coordinate system."]
+ [motif
+ :ref
+ "A motif entity which is mapped to a sequence by this homology."]
+ [rnai
+ :ref
+ "An RNAi entity which is mapped to a sequence by this homology."]
+ [oligo-set
+ :ref
+ "An oligo-set which is mapped to a sequence by this homology."]
+ [protein
+ :ref
+ "Protein entity representing the target of a peptide homology."]
+ [strand
+ :enum
+ [:negative :positive]
+ "Token designating the strand or orientation of this homology on the target's coordinate system. Should only be used in situations where a negative-to-negative alignment would be meaningful (e.g. tblastx)"]
+ [ms-peptide
+ :ref
+ "Mass-spec-peptide which is mapped to a sequence by this homology."]
+ [align-id :string "Alignment ID to emit in GFF dumps."]
+ [sage
+ :ref
+ "SAGE-tag which is mapped to a sequence by this homology."]))
+
+(schema
+ map
+ (fields
+ [id :string :unique-identity]
+ [no-cache :boolean]
+ [non-graphic :boolean]
+ [title :string :indexed]
+ [flipped :boolean]
+ [unit :string]
+ [centre :ref :component]
+ [extent :ref :component]
+ [inherits-from-map :ref]
+ [author :string :many]
+ [main-locus :ref :many]
+ [map :ref :many :component]
+ [includes :ref :many]
+ [embl-chromosome :string]))
+
+(schema map.centre (fields [min :double] [max :double]))
+
+(schema map.extent (fields [min :double] [max :double]))
+
+(schema map.map (fields [map :ref]))
+
+(schema
+ map-position
+ (fields
+ [id :string :unique-identity]
+ [position :ref :component]
+ [left :ref :component]
+ [right :ref :component]
+ [multi-position :ref :many :component]
+ [multi-ends :ref :many :component]
+ [with-locus :ref :component]
+ [with-clone :ref :component]))
+
+(schema map-position.position (fields [float :double]))
+
+(schema map-position.left (fields [float :double]))
+
+(schema map-position.right (fields [float :double]))
+
+(schema map-position.multi-position (fields [float :double]))
+
+(schema map-position.multi-ends (fields [min :double] [max :double]))
+
+(schema map-position.with-locus (fields [locus :ref]))
+
+(schema map-position.with-clone (fields [clone :ref]))
+
+(schema
+ map-error
+ (fields [id :string :unique-identity] [error :double]))
+
+(schema
+ map-offset
+ (fields [id :string :unique-identity] [relative :ref :component]))
+
+(schema
+ gene-class
+ (fields
+ [id :string :unique-identity]
+ [evidence :ref :component]
+ [phenotype :string :indexed :many]
+ [description :string :indexed :many]
+ [designating-laboratory :ref]
+ [former-designating-laboratory :ref :many :component]
+ [old-member :string :indexed :many]
+ [main-name :ref :many]
+ [remark :ref :many :component]))
+
+(schema
+ gene-class.former-designating-laboratory
+ (fields [until :instant] [laboratory :ref]))
+
+(schema gene-class.remark (fields [text :string :indexed]))
+
+(schema
+ locus
+ (fields
+ [id :string :unique-identity]
+ [evidence :ref :component]
+ [other-name :ref :many :component]
+ [species :ref]
+ [snp :string :many]
+ [status :string :many]
+ [snp-assay :ref :many :component]
+ [rflp :string :many]
+ [transposon-insertion :string :many]
+ [detection-method :string :many]
+ [map :ref :component]
+ [well-ordered :boolean]
+ [laboratory :ref :many]
+ [remark :ref :many :component]))
+
+(schema locus.other-name (fields [text :string :indexed]))
+
+(schema
+ locus.snp-assay
+ (fields [pcr-product :ref] [text :string :indexed]))
+
+(schema locus.map (fields [map :ref]))
+
+(schema locus.remark (fields [text :string :indexed]))
+
+(schema
+ gene
+ (fields
+ [id :string :unique-identity]
+ [evidence :ref :component]
+ [version :long]
+ [cgc-name :ref :component]
+ [sequence-name :string :indexed]
+ [molecular-name :string :indexed :many]
+ [other-name :ref :many :component]
+ [public-name :string :indexed]
+ [database :ref :many :component]
+ [species :ref]
+ [version-change :ref :many :component]
+ [acquires-merge :ref :many]
+ [split-into :ref :many]
+ [transposon-in-origin :boolean]
+ [status :ref :component]
+ [biotype :ref]
+ [gene-class :ref]
+ [laboratory :ref :many]
+ [cloned-by :ref :component]
+ [reference-allele :ref :many :component]
+ [legacy-information :ref :many :component]
+ [complementation-data :string :many]
+ [strain :ref :many]
+ [rnaseq :ref :many :component]
+ [go-term :ref :many :component]
+ [ortholog :ref :many :component]
+ [paralog :ref :many :component]
+ [ortholog-other :ref :many :component]
+ [provisional-description :ref :many :component]
+ [concise-description :ref :many :component]
+ [other-description :ref :many :component]
+ [automated-description :ref :many :component]
+ [sequence-features :ref :many :component]
+ [functional-pathway :ref :many :component]
+ [functional-physical-interaction :ref :many :component]
+ [biological-process :ref :many :component]
+ [molecular-function :ref :many :component]
+ [expression :ref :many :component]
+ [disease-experimental-model :ref :many :component]
+ [disease-potential-model :ref :many :component]
+ [disease-relevance :ref :many :component]
+ [corresponding-cds :ref :many :component]
+ [corresponding-cds-history :ref :many]
+ [corresponding-transcript :ref :many :component]
+ [corresponding-transcript-history :ref :many]
+ [corresponding-pseudogene :ref :many :component]
+ [corresponding-pseudogene-history :ref :many]
+ [corresponding-transposon :ref :many :component]
+ [other-sequence :ref :many :component]
+ [map :ref :component]
+ [well-ordered :boolean]
+ [hide-under :ref :many]
+ [interpolated-map-position :ref :component]
+ [landmark-gene :boolean]
+ [pseudo-map-position :boolean]
+ [reference :ref :many]
+ [remark :ref :many :component]))
+
+(schema gene.cgc-name (fields [text :string :indexed]))
+
+(schema gene.other-name (fields [text :string :indexed]))
+
+(schema
+ gene.database
+ (fields [database :ref] [field :ref] [accession :string :indexed]))
+
+(schema
+ gene.version-change
+ (fields [version :long] [date :instant] [person :ref]))
+
+(schema gene.status (fields [status :enum [:live :suppressed :dead]]))
+
+(schema gene.reference-allele (fields [variation :ref]))
+
+(schema gene.legacy-information (fields [text :string]))
+
+(schema gene.rnaseq (fields [stage :ref] [fpkm :double]))
+
+(schema gene.go-term (fields [go-term :ref] [go-code :ref]))
+
+(schema gene.ortholog (fields [gene :ref] [species :ref]))
+
+(schema gene.paralog (fields [gene :ref] [species :ref]))
+
+(schema gene.ortholog-other (fields [protein :ref]))
+
+(schema gene.provisional-description (fields [text :string :indexed]))
+
+(schema gene.concise-description (fields [text :string :indexed]))
+
+(schema gene.other-description (fields [text :string :indexed]))
+
+(schema gene.automated-description (fields [text :string :indexed]))
+
+(schema gene.sequence-features (fields [text :string :indexed]))
+
+(schema gene.functional-pathway (fields [text :string :indexed]))
+
+(schema
+ gene.functional-physical-interaction
+ (fields [text :string :indexed]))
+
+(schema gene.biological-process (fields [text :string :indexed]))
+
+(schema gene.molecular-function (fields [text :string :indexed]))
+
+(schema gene.expression (fields [text :string :indexed]))
+
+(schema
+ gene.disease-experimental-model
+ (fields [do-term :ref] [species :ref]))
+
+(schema
+ gene.disease-potential-model
+ (fields [do-term :ref] [species :ref]))
+
+(schema
+ gene.disease-relevance
+ (fields [note :string :indexed] [species :ref]))
+
+(schema gene.corresponding-cds (fields [cds :ref]))
+
+(schema gene.corresponding-transcript (fields [transcript :ref]))
+
+(schema gene.corresponding-pseudogene (fields [pseudogene :ref]))
+
+(schema gene.corresponding-transposon (fields [transposon :ref]))
+
+(schema gene.other-sequence (fields [sequence :ref]))
+
+(schema gene.map (fields [map :ref]))
+
+(schema
+ gene.interpolated-map-position
+ (fields [map :ref] [position :double]))
+
+(schema gene.remark (fields [text :string :indexed]))
+
+(schema
+ gene-cluster
+ (fields
+ [id :string :unique-identity]
+ [description :string :indexed :many]
+ [contains-gene :ref :many]
+ [analysis :ref :many]
+ [reference :ref :many :component]))
+
+(schema gene-cluster.reference (fields [paper :ref]))
+
+(schema
+ gene-history-action
+ (fields
+ [id :string :unique-identity]
+ [created :boolean]
+ [killed :boolean]
+ [suppressed :boolean]
+ [resurrected :boolean]
+ [merged-into :ref]
+ [acquires-merge :ref]
+ [split-from :ref]
+ [split-into :ref]
+ [imported :string :many]
+ [changed-class :ref :many :component]
+ [transposon-in-origin :boolean]
+ [cgc-name-change :string]
+ [sequence-name-change :string]
+ [other-name-change :string]))
+
+(schema
+ gene-history-action.changed-class
+ (fields [old :string] [new :string]))
+
+(schema
+ interaction
+ (fields
+ [id :string :unique-identity]
+ [type
+ :enum
+ [:genetic
+ :genetic:mutual-enhancement
+ :genetic:positive-genetic
+ :genetic:neutral-genetic
+ :genetic:partial-suppression
+ :genetic:complete-unilateral-suppression
+ :genetic:unilateral-oversuppression
+ :genetic:minimal-epistasis
+ :physical:proteinrna
+ :genetic:mutual-suppression
+ :genetic:neutral-epistasis
+ :genetic:negative-genetic
+ :genetic:maximal-epistasis
+ :genetic:asynthetic
+ :regulatory:change-of-localization
+ :physical:proteinprotein
+ :regulatory:change-of-expression-level
+ :genetic:quantitative-epistasis
+ :genetic:epistasis
+ :genetic:genetic-interaction
+ :genetic:mutual-oversuppression
+ :genetic:suppression-enhancement
+ :genetic:positive-epistasis
+ :genetic:qualitative-epistasis
+ :genetic:oversuppression-enhancement
+ :regulatory
+ :genetic:suppression
+ :genetic:phenotype-bias
+ :genetic:complete-mutual-suppression
+ :genetic:partial-mutual-suppression
+ :predicted
+ :genetic:synthetic
+ :genetic:partial-unilateral-suppression
+ :genetic:oversuppression
+ :genetic:unilateral-suppression
+ :genetic:no-interaction
+ :genetic:enhancement
+ :genetic:complete-suppression
+ :physical:proteindna
+ :genetic:opposing-epistasis
+ :physical
+ :genetic:unilateral-enhancement]
+ :many]
+ [pcr-interactor :ref :many :component]
+ [sequence-interactor :ref :many :component]
+ [interactor-overlapping-cds :ref :many :component]
+ [interactor-overlapping-gene :ref :many :component]
+ [interactor-overlapping-protein :ref :many :component]
+ [molecule-interactor :ref :many :component]
+ [other-interactor :ref :many :component]
+ [rearrangement :ref :many :component]
+ [feature-interactor :ref :many :component]
+ [variation-interactor :ref :many :component]
+ [interaction-summary :ref :many :component]
+ [detection-method :ref :many :component]
+ [library-screened :ref :many :component]
+ [from-laboratory :ref]
+ [from-company :string :indexed]
+ [regulation-level
+ :enum
+ [:post-transcriptional :transcriptional :post-translational]
+ :many]
+ [regulation-result :ref :many :component]
+ [confidence-description :string :many]
+ [p-value :double]
+ [log-likelihood-score :double]
+ [throughput :enum [:high-throughput :low-throughput]]
+ [interaction-rnai :ref :many]
+ [interaction-phenotype :ref :many]
+ [unaffiliated-variation :ref :many]
+ [unaffiliated-transgene :ref :many]
+ [unaffiliated-antibody :ref :many]
+ [unaffiliated-expr-pattern :ref :many]
+ [unaffiliated-construct :ref :many]
+ [database :ref :many :component]
+ [paper :ref :many]
+ [antibody-remark :string :indexed :many]
+ [historical-gene :ref :many :component]
+ [remark :ref :many :component]))
+
+(schema interaction.pcr-interactor (fields [pcr-product :ref]))
+
+(schema interaction.sequence-interactor (fields [sequence :ref]))
+
+(schema interaction.interactor-overlapping-cds (fields [cds :ref]))
+
+(schema interaction.interactor-overlapping-gene (fields [gene :ref]))
+
+(schema
+ interaction.interactor-overlapping-protein
+ (fields [protein :ref]))
+
+(schema interaction.molecule-interactor (fields [molecule :ref]))
+
+(schema interaction.other-interactor (fields [text :string :indexed]))
+
+(schema interaction.rearrangement (fields [rearrangement :ref]))
+
+(schema interaction.feature-interactor (fields [feature :ref]))
+
+(schema interaction.variation-interactor (fields [variation :ref]))
+
+(schema
+ interaction.interaction-summary
+ (fields [text :string :indexed]))
+
+(schema
+ interaction.detection-method
+ (fields
+ [value
+ :enum
+ [:dnase-i-footprinting
+ :affinity-capture-western
+ :antibody
+ :protein-fragment-complementation-assay
+ :chromatin-immunoprecipitation
+ :copurification
+ :colocalization
+ :in-situ
+ :affinity-capture-luminescence
+ :far-western
+ :fluorescence-resonance-energy-transfer
+ :western
+ :other-method
+ :reconstituted-complex
+ :directed-yeast-one-hybrid
+ :cocrystal-structure
+ :yeast-one-hybrid
+ :affinity-capture-rna
+ :transgene
+ :protein-rna
+ :electrophoretic-mobility-shift-assay
+ :yeast-two-hybrid
+ :construct
+ :northern
+ :cofractionation
+ :affinity-capture-ms
+ :biochemical-activity
+ :rt-pcr
+ :protein-peptide
+ :reporter-gene]]
+ [text :string]))
+
+(schema
+ interaction.library-screened
+ (fields [library :string] [version :long]))
+
+(schema
+ interaction.regulation-result
+ (fields
+ [value
+ :enum
+ [:does-not-regulate :negative-regulate :positive-regulate]]))
+
+(schema
+ interaction.database
+ (fields [database :ref] [field :ref] [accession :string :indexed]))
+
+(schema interaction.historical-gene (fields [gene :ref] [text :string]))
+
+(schema interaction.remark (fields [text :string :indexed]))
+
+(schema
+ interactor-info
+ (fields
+ [id :string :unique-identity]
+ [interactor-type
+ :enum
+ [:trans-regulator
+ :cis-regulator
+ :bait
+ :affected
+ :cis-regulated
+ :non-directional
+ :effector
+ :target
+ :trans-regulated]
+ :many]
+ [expr-pattern :ref :many]
+ [transgene :ref :many]
+ [construct :ref :many]
+ [antibody :ref :many]
+ [inferred-automatically :string :many]))
+
+(schema
+ balancer
+ (fields
+ [id :string :unique-identity]
+ [from-left-end :boolean]
+ [to-right-end :boolean]
+ [locus :ref :many]
+ [gene :ref :many]))
+
+(schema
+ rearrangement
+ (fields
+ [id :string :unique-identity]
+ [evidence :ref :component]
+ [other-name :string :indexed :many]
+ [variation :ref :many]
+ [type
+ :enum
+ [:translocation
+ :inversion
+ :duplication:free-dup
+ :deletion
+ :compound
+ :duplication
+ :introgression]
+ :many]
+ [phenotype :ref :many :component]
+ [phenotype-not-observed :ref :many :component]
+ [balances :ref :many :component]
+ [marked-by-variation :ref :many]
+ [marked-by-transgene :ref :many]
+ [marked-by-other :string :indexed :many]
+ [reference-strain :ref :many]
+ [species :ref]
+ [remark :ref :many :component]
+ [author :ref :many]
+ [person :ref :many]
+ [date :instant]
+ [mutagen :ref :component]
+ [source-rearrangement :ref]
+ [map :ref :many :component]
+ [gene-inside :ref :many :component]
+ [locus-inside :ref :many :component]
+ [rearr-inside :ref :many]
+ [gene-outside :ref :many :component]
+ [locus-outside :ref :many :component]
+ [rearr-outside :ref :many]
+ [pos-neg-data :ref :many]
+ [two-point :ref :many]
+ [multi-point :ref :many]
+ [hide-under :ref]
+ [location :ref :many :component]
+ [url :string :many]
+ [strain :ref :many]
+ [reference :ref :many :component]))
+
+(schema rearrangement.phenotype (fields [phenotype :ref]))
+
+(schema rearrangement.phenotype-not-observed (fields [phenotype :ref]))
+
+(schema rearrangement.balances (fields [map :ref]))
+
+(schema rearrangement.remark (fields [text :string :indexed]))
+
+(schema rearrangement.mutagen (fields [name :string] [dose :string]))
+
+(schema rearrangement.map (fields [map :ref]))
+
+(schema rearrangement.gene-inside (fields [gene :ref]))
+
+(schema rearrangement.locus-inside (fields [locus :ref] [author :ref]))
+
+(schema rearrangement.gene-outside (fields [gene :ref]))
+
+(schema rearrangement.locus-outside (fields [locus :ref] [author :ref]))
+
+(schema rearrangement.location (fields [laboratory :ref]))
+
+(schema rearrangement.reference (fields [paper :ref]))
+
+(schema
+ strain
+ (fields
+ [id :string :unique-identity]
+ [evidence :ref :component]
+ [genotype :string]
+ [other-name :ref :many :component]
+ [database :ref :many :component]
+ [inbreeding-state :enum [:multifemale :selfed :inbred :isofemale]]
+ [outcrossed :string]
+ [mutagen :string :many]
+ [strain-history :string :many]
+ [date-first-frozen :instant]
+ [cgc-received :instant :many]
+ [phenotype :ref :many :component]
+ [phenotype-not-observed :ref :many :component]
+ [location :ref :many :component]
+ [made-by :ref :many]
+ [contact :ref :many]
+ [remark :ref :many :component]
+ [reference :ref :many :component]
+ [species :ref]
+ [ncbi-taxonomy :long]
+ [wild-isolate :boolean]
+ [geolocation :ref :component]
+ [elevation :ref :component]
+ [place :string :indexed]
+ [landscape
+ :enum
+ [:botanical-garden-zoo
+ :oasis
+ :agricultural-land
+ :forest
+ :urban-garden
+ :wet-shrubland
+ :dry-shrubland
+ :wild-grassland
+ :rural-garden]]
+ [substrate :string :indexed]
+ [associated-organisms :ref :many]
+ [life-stage :ref :many]
+ [log-size-of-population :double]
+ [sampled-by :string :many]
+ [isolated-by :ref :many]
+ [date :instant]
+ [picture :ref :many]))
+
+(schema strain.other-name (fields [text :string :indexed]))
+
+(schema
+ strain.database
+ (fields [database :ref] [field :ref] [accession :string :indexed]))
+
+(schema strain.phenotype (fields [phenotype :ref]))
+
+(schema strain.phenotype-not-observed (fields [phenotype :ref]))
+
+(schema strain.location (fields [laboratory :ref]))
+
+(schema strain.remark (fields [text :string :indexed]))
+
+(schema strain.reference (fields [paper :ref]))
+
+(schema
+ strain.geolocation
+ (fields [latitude :double] [longitude :double]))
+
+(schema strain.elevation (fields [float :double]))
+
+(schema
+ position-confidence
+ (fields
+ [id :string :unique-identity]
+ [exact :boolean]
+ [approximate :double]
+ [inferred-from-gps :boolean]))
+
+(schema
+ lab-location
+ (fields
+ [id :string :unique-identity]
+ [freezer :string :many]
+ [liquid-n2 :string :many]
+ [minus70 :string :many]
+ [remark :ref :many :component]))
+
+(schema lab-location.remark (fields [text :string :indexed]))
+
+(schema
+ clone
+ (fields
+ [id :string :unique-identity]
+ [evidence :ref :component]
+ [species :ref]
+ [reference :ref :many :component]
+ [produced-by-person :ref :many]
+ [produced-by-author :ref :many]
+ [general-remark :string :indexed :many]
+ [y-remark :string :indexed :many]
+ [pcr-remark :string :indexed :many]
+ [map :ref :many :component]
+ [pmap :ref :component]
+ [positive-gene :ref :many :component]
+ [positive-variation :ref :many :component]
+ [inside-rearr :ref :many :component]
+ [hybridizes-to :ref :many :component]
+ [hybridizes-weak :ref :many :component]
+ [negative-gene :ref :many :component]
+ [negative-locus :ref :many :component]
+ [outside-rearr :ref :many :component]
+ [does-not-hybridize-to :ref :many :component]
+ [in-strain :ref :many]
+ [mutation :string :indexed :many]
+ [primer1 :string :indexed :many]
+ [primer2 :string :indexed :many]
+ [resistance-marker :string :indexed :many]
+ [seq-length :long]
+ [gel-length :double]
+ [insert-length :long]
+ [backbone-length :long]
+ [location :ref :many :component]
+ [url :string :many]
+ [gel-number :long]
+ [canonical-for :ref :many :component]
+ [bands :ref :component]
+ [gel :ref :many :component]
+ [chromosome :ref]
+ [vaxmap :double]
+ [in-situ :ref :component]
+ [cosmid-grid :boolean]
+ [canon-for-cosmid :boolean]
+ [flag :long]
+ [autopos :boolean]
+ [pattern :string :indexed :many]
+ [contains :ref :many :component]
+ [contained-in :ref :many]
+ [best-match :string :indexed]
+ [shotgun :instant]
+ [finished :instant]
+ [accession-number :string :indexed]
+ [database :ref :many :component]
+ [type :ref :component]
+ [vector-type :string :indexed :many]
+ [derived-from :ref :many]
+ [ligation :string :indexed :many]))
+
+(schema clone.reference (fields [paper :ref]))
+
+(schema clone.map (fields [map :ref]))
+
+(schema clone.pmap (fields [contig :ref] [pos1 :long] [pos2 :long]))
+
+(schema clone.positive-gene (fields [gene :ref]))
+
+(schema
+ clone.positive-variation
+ (fields [variation :ref] [author :ref]))
+
+(schema clone.inside-rearr (fields [rearrangement :ref] [author :ref]))
+
+(schema clone.hybridizes-to (fields [clone :ref] [grid :ref]))
+
+(schema clone.hybridizes-weak (fields [clone :ref] [grid :ref]))
+
+(schema clone.negative-gene (fields [gene :ref]))
+
+(schema clone.negative-locus (fields [locus :ref] [author :ref]))
+
+(schema clone.outside-rearr (fields [rearrangement :ref] [author :ref]))
+
+(schema clone.does-not-hybridize-to (fields [clone :ref] [grid :ref]))
+
+(schema clone.location (fields [laboratory :ref]))
+
+(schema
+ clone.canonical-for
+ (fields [clone :ref] [start :long] [stop :long]))
+
+(schema clone.bands (fields [start :long] [stop :long]))
+
+(schema clone.gel (fields [motif :ref]))
+
+(schema clone.in-situ (fields [start :long] [stop :long]))
+
+(schema clone.contains (fields [clone :ref] [text :string]))
+
+(schema
+ clone.database
+ (fields [database :ref] [field :ref] [accession :string :indexed]))
+
+(schema
+ clone.type
+ (fields
+ [value :enum [:cosmid :yac :plasmid :cdna :fosmid :other]]
+ [text :string]))
+
+(schema
+ lane
+ (fields
+ [id :string :unique-identity]
+ [bands :double]
+ [band-lengths :double]
+ [band :ref :many :component]))
+
+(schema lane.band (fields [float :double] [text :string]))
+
+(schema
+ grid
+ (fields
+ [id :string :unique-identity]
+ [title :string :indexed :many]
+ [columns :long]
+ [lines-at :ref :component]
+ [space-at :ref :component]
+ [no-stagger :boolean]
+ [size :ref :component]
+ [a1-labelling :boolean]
+ [xy-labelling :ref :component]
+ [row :ref :many :component]))
+
+(schema grid.lines-at (fields [x :long] [y :long]))
+
+(schema grid.space-at (fields [x :long] [y :long]))
+
+(schema grid.size (fields [x :long] [y :long]))
+
+(schema grid.xy-labelling (fields [x :string] [y :string]))
+
+(schema grid.row (fields [int :long]))
+
+(schema
+ grid-data
+ (fields
+ [id :string :unique-identity]
+ [mapper :ref :many]
+ [laboratory :ref :many]
+ [date :instant]
+ [hybridizes-to :ref :many]
+ [positive-product :ref :many]
+ [grid :ref]
+ [clone :ref]
+ [default-negative :boolean]))
+
+(schema
+ grid-row
+ (fields
+ [id :string :unique-identity]
+ [clone :ref]
+ [mixed :ref :component]))
+
+(schema
+ mixed-grid-row
+ (fields [id :string :unique-identity] [clone :ref :component]))
+
+(schema mixed-grid-row.clone (fields [clone :ref]))
+
+(schema
+ contig
+ (fields
+ [id :string :unique-identity]
+ [map :ref :many :component]
+ [pmap :ref :component]))
+
+(schema contig.map (fields [map :ref]))
+
+(schema contig.pmap (fields [start :long] [stop :long]))
+
+(schema
+ species
+ (fields
+ [id :string :unique-identity]
+ [short-name :string]
+ [other-name :string :many]
+ [g-species :string]
+ [ncbi-taxonomy :long]
+ [assembly :ref :many]))
+
+(schema
+ two-point-data
+ (fields
+ [id :string :unique-identity]
+ [evidence :ref :component]
+ [genotype :string]
+ [results :string]
+ [mapper :ref :many]
+ [laboratory :ref :many]
+ [date :instant]
+ [temperature :string]
+ [gene-1 :ref :component]
+ [locus-1 :ref :component]
+ [allele-1 :ref]
+ [rearrangement-1 :ref]
+ [gene-2 :ref :component]
+ [locus-2 :ref :component]
+ [allele-2 :ref]
+ [rearrangement-2 :ref]
+ [full :ref :component]
+ [one-recombinant :ref :component]
+ [selected :ref :component]
+ [one-all :ref :component]
+ [recs-all :ref :component]
+ [one-let :ref :component]
+ [tested :ref :component]
+ [selected-trans :ref :component]
+ [backcross :ref :component]
+ [back-one :ref :component]
+ [sex-full :ref :component]
+ [sex-one :ref :component]
+ [sex-cis :ref :component]
+ [dom-one :ref :component]
+ [dom-selected :ref :component]
+ [dom-semi :ref :component]
+ [dom-let :ref :component]
+ [direct :ref :component]
+ [complex-mixed :ref :component]
+ [calc-distance :double]
+ [calc-lower-conf :double]
+ [calc-upper-conf :double]
+ [min :double]
+ [distance :double]
+ [max :double]
+ [error :double]
+ [linkage :string]
+ [remark :ref :many :component]))
+
+(schema two-point-data.gene-1 (fields [gene :ref] [variation :ref]))
+
+(schema two-point-data.locus-1 (fields [locus :ref] [variation :ref]))
+
+(schema two-point-data.gene-2 (fields [gene :ref] [variation :ref]))
+
+(schema two-point-data.locus-2 (fields [locus :ref] [variation :ref]))
+
+(schema
+ two-point-data.full
+ (fields [wt :long] [x :long] [y :long] [xy :long]))
+
+(schema two-point-data.one-recombinant (fields [wt :long] [x :long]))
+
+(schema two-point-data.selected (fields [x :long] [xy :long]))
+
+(schema two-point-data.one-all (fields [x :long] [all :long]))
+
+(schema
+ two-point-data.recs-all
+ (fields [x :long] [y :long] [all :long]))
+
+(schema two-point-data.one-let (fields [x :long] [all :long]))
+
+(schema two-point-data.tested (fields [x :long] [h :long]))
+
+(schema two-point-data.selected-trans (fields [x :long] [xy :long]))
+
+(schema
+ two-point-data.backcross
+ (fields [wt :long] [x :long] [y :long] [xy :long]))
+
+(schema two-point-data.back-one (fields [wt :long] [x :long]))
+
+(schema
+ two-point-data.sex-full
+ (fields [wt :long] [x :long] [y :long] [xy :long]))
+
+(schema two-point-data.sex-one (fields [wt :long] [x :long]))
+
+(schema two-point-data.sex-cis (fields [x :long] [all :long]))
+
+(schema two-point-data.dom-one (fields [wt :long] [non-wt :long]))
+
+(schema two-point-data.dom-selected (fields [wt :long] [x :long]))
+
+(schema two-point-data.dom-semi (fields [xd :long] [all :long]))
+
+(schema two-point-data.dom-let (fields [wt :long] [all :long]))
+
+(schema two-point-data.direct (fields [r :long] [t :long]))
+
+(schema two-point-data.complex-mixed (fields [x :long] [all :long]))
+
+(schema two-point-data.remark (fields [text :string :indexed]))
+
+(schema
+ pos-neg-data
+ (fields
+ [id :string :unique-identity]
+ [evidence :ref :component]
+ [genotype :string]
+ [results :string]
+ [mapper :ref :many]
+ [laboratory :ref :many]
+ [date :instant]
+ [gene-1 :ref :component]
+ [locus-1 :ref :component]
+ [rearrangement-1 :ref]
+ [allele-1 :ref]
+ [clone-1 :ref]
+ [gene-2 :ref :component]
+ [locus-2 :ref :component]
+ [rearrangement-2 :ref]
+ [allele-2 :ref]
+ [clone-2 :ref]
+ [calculation :enum [:negative :positive]]
+ [remark :ref :many :component]))
+
+(schema pos-neg-data.gene-1 (fields [gene :ref] [variation :ref]))
+
+(schema pos-neg-data.locus-1 (fields [locus :ref] [variation :ref]))
+
+(schema pos-neg-data.gene-2 (fields [gene :ref] [variation :ref]))
+
+(schema pos-neg-data.locus-2 (fields [locus :ref] [variation :ref]))
+
+(schema pos-neg-data.remark (fields [text :string :indexed]))
+
+(schema
+ multi-pt-data
+ (fields
+ [id :string :unique-identity]
+ [evidence :ref :component]
+ [genotype :string]
+ [mapper :ref :many]
+ [laboratory :ref :many]
+ [date :instant]
+ [gene-a :ref :component]
+ [locus-a :ref :component]
+ [allele-a :ref]
+ [rearrangement-a :ref]
+ [gene-b :ref :component]
+ [locus-b :ref :component]
+ [allele-b :ref]
+ [rearrangement-b :ref]
+ [gene :ref :many :component]
+ [locus :ref :many :component]
+ [a-non-b :ref :component]
+ [b-non-a :ref :component]
+ [combined :ref :component]
+ [old-cgc-results :string :many]
+ [remark :ref :many :component]))
+
+(schema multi-pt-data.gene-a (fields [gene :ref] [variation :ref]))
+
+(schema multi-pt-data.locus-a (fields [locus :ref] [variation :ref]))
+
+(schema multi-pt-data.gene-b (fields [gene :ref] [variation :ref]))
+
+(schema multi-pt-data.locus-b (fields [locus :ref] [variation :ref]))
+
+(schema multi-pt-data.gene (fields [gene :ref] [variation :ref]))
+
+(schema multi-pt-data.locus (fields [locus :ref] [variation :ref]))
+
+(schema multi-pt-data.remark (fields [text :string :indexed]))
+
+(schema
+ multi-counts
+ (fields
+ [id :string :unique-identity]
+ [gene :ref :component]
+ [locus :ref :component]
+ [allele :ref :component]
+ [rearrangement :ref :component]
+ [transgene :ref :component]))
+
+(schema multi-counts.gene (fields [gene :ref] [int :long]))
+
+(schema multi-counts.locus (fields [locus :ref] [int :long]))
+
+(schema multi-counts.allele (fields [variation :ref] [int :long]))
+
+(schema
+ multi-counts.rearrangement
+ (fields [rearrangement :ref] [int :long]))
+
+(schema multi-counts.transgene (fields [transgene :ref] [int :long]))
+
+(schema
+ evidence
+ (fields
+ [id :string :unique-identity]
+ [paper-evidence :ref :many]
+ [published-as :string :indexed :many]
+ [person-evidence :ref :many]
+ [author-evidence :ref :many :component]
+ [accession-evidence :ref :many :component]
+ [protein-id-evidence :string :indexed :many]
+ [go-term-evidence :ref :many]
+ [expr-pattern-evidence :ref :many]
+ [microarray-results-evidence :ref :many]
+ [rnai-evidence :ref :many]
+ [cgc-data-submission :boolean]
+ [curator-confirmed :ref :many]
+ [inferred-automatically :string :many]
+ [date-last-updated :instant]
+ [feature-evidence :ref :many]
+ [laboratory-evidence :ref :many]
+ [from-analysis :ref :many]
+ [variation-evidence :ref :many]
+ [mass-spec-evidence :ref :many]
+ [sequence-evidence :ref :many]
+ [remark :string :indexed :many]))
+
+(schema evidence.author-evidence (fields [author :ref] [note :string]))
+
+(schema
+ evidence.accession-evidence
+ (fields [database :ref] [accession :string :indexed]))
+
+(schema
+ go-annotation
+ (fields
+ [id :string :unique-identity]
+ [gene :ref]
+ [go-term :ref]
+ [go-code :ref]
+ [annotation-relation
+ :enum
+ [:enables
+ :contributes-to
+ :not
+ :involved-in
+ :part-of
+ :colocalizes-with]
+ :many]
+ [interacting-gene :ref :many]
+ [inferred-from-go-term :ref :many]
+ [motif :ref :many]
+ [rnai-result :ref :many]
+ [variation :ref :many]
+ [phenotype :ref :many]
+ [database :ref :many :component]
+ [life-stage-relation :ref :many :component]
+ [gene-relation :ref :many :component]
+ [molecule-relation :ref :many :component]
+ [anatomy-relation :ref :many :component]
+ [go-term-relation :ref :many :component]
+ [annotation-isoform :ref :many :component]
+ [interacting-species :ref :many :component]
+ [reference :ref]
+ [go-reference :ref :many :component]
+ [contributed-by :ref]
+ [date-last-updated :instant]))
+
+(schema
+ go-annotation.database
+ (fields [database :ref] [database-field :ref] [text :string :indexed]))
+
+(schema
+ go-annotation.life-stage-relation
+ (fields [text :string :indexed] [life-stage :ref]))
+
+(schema
+ go-annotation.gene-relation
+ (fields [text :string :indexed] [gene :ref]))
+
+(schema
+ go-annotation.molecule-relation
+ (fields [text :string :indexed] [molecule :ref]))
+
+(schema
+ go-annotation.anatomy-relation
+ (fields [text :string :indexed] [anatomy-term :ref]))
+
+(schema
+ go-annotation.go-term-relation
+ (fields [text :string :indexed] [go-term :ref]))
+
+(schema
+ go-annotation.annotation-isoform
+ (fields [text :string :indexed] [protein :ref]))
+
+(schema
+ go-annotation.interacting-species
+ (fields [species :ref] [strain :ref]))
+
+(schema
+ go-annotation.go-reference
+ (fields [database :ref] [database-field :ref] [text :string :indexed]))
+
+(schema
+ go-term
+ (fields
+ [id :string :unique-identity]
+ [name :string :indexed :many]
+ [definition :string :indexed :many]
+ [alt-id :string :indexed :many]
+ [synonym :ref :many :component]
+ [status :enum [:valid :obsolete]]
+ [type
+ :enum
+ [:cellular-component :biological-process :molecular-function]]
+ [instance :ref :many]
+ [component :ref :many]
+ [ancestor :ref :many]
+ [version :string]))
+
+(schema
+ go-term.synonym
+ (fields
+ [scope :enum [:related :exact :narrow :broad]]
+ [text :string :indexed]))
+
+(schema
+ go-code
+ (fields
+ [id :string :unique-identity]
+ [description :string :indexed :many]
+ [remark :ref :many :component]))
+
+(schema go-code.remark (fields [text :string :indexed]))
+
+(schema
+ so-term
+ (fields
+ [id :string :unique-identity]
+ [name :string :indexed]
+ [definition :string :indexed]
+ [synonym :string :indexed :many]
+ [so-version :string :indexed :many]
+ [located-sequence-feature
+ :enum
+ [:junction :region :sequence-alteration]]
+ [is-a :ref :many]
+ [part-of :ref :many]
+ [derived-from :ref :many]
+ [member-of :ref :many]
+ [ancestor :ref :many]))
+
+(schema
+ ace2so
+ (fields
+ [id :string :unique-identity]
+ [description :string]
+ [exons :ref]
+ [introns :ref]
+ [coding-region :ref]
+ [no-span :boolean]
+ [so-parent-obj-tag :string]
+ [so-children :boolean]))
+
+(schema
+ do-term
+ (fields
+ [id :string :unique-identity]
+ [name :string :indexed]
+ [status :enum [:valid :obsolete]]
+ [alternate-id :string :indexed :many]
+ [definition :string :indexed]
+ [comment :string :many]
+ [synonym :ref :many :component]
+ [is-a :ref :many]
+ [database :ref :many :component]
+ [type
+ :enum
+ [:tick-borne-infectious-disease
+ :sexually-transmitted-infectious-disease
+ :zoonotic-infectious-disease
+ :gram-negative-bacterial-infectious-disease
+ :gram-positive-bacterial-infectious-disease
+ :gold]
+ :many]
+ [version :string]))
+
+(schema
+ do-term.synonym
+ (fields
+ [scope :enum [:related :exact :broad :narrow]]
+ [text :string :indexed]))
+
+(schema
+ do-term.database
+ (fields [database :ref] [field :ref] [accession :string :indexed]))
+
+(schema
+ pato-term
+ (fields
+ [id :string :unique-identity]
+ [name :string :indexed :many]
+ [definition :string :indexed :many]
+ [alt-id :string :indexed :many]
+ [synonym :string :indexed :many]
+ [status :enum [:valid :obsolete]]
+ [child :boolean]
+ [parent :boolean]
+ [version :string]))
+
+(schema
+ ao-code
+ (fields
+ [id :string :unique-identity]
+ [description :string :indexed :many]
+ [remark :ref :many :component]))
+
+(schema ao-code.remark (fields [text :string :indexed]))
+
+(schema
+ neurodata
+ (fields
+ [id :string :unique-identity]
+ [send :ref :many :component]
+ [send-joint :ref :many :component]
+ [receive :ref :many :component]
+ [receive-joint :ref :many :component]
+ [gap-junction :ref :many :component]
+ [evidence :ref :component]))
+
+(schema neurodata.send (fields [series :string] [count :long]))
+
+(schema neurodata.send-joint (fields [series :string] [count :long]))
+
+(schema neurodata.receive (fields [series :string] [count :long]))
+
+(schema neurodata.receive-joint (fields [series :string] [count :long]))
+
+(schema neurodata.gap-junction (fields [series :string] [count :long]))
+
+(schema
+ neuro-location
+ (fields [id :string :unique-identity] [section :ref :many :component]))
+
+(schema
+ neuro-location.section
+ (fields [first-section :long] [last-section :long] [remark :string]))
+
+(schema
+ reconstruction
+ (fields
+ [id :string :unique-identity]
+ [anatomy-term :ref :many]
+ [author :ref :many]
+ [date :instant]
+ [remark :ref :many :component]
+ [description :ref :many]))
+
+(schema reconstruction.remark (fields [text :string :indexed]))
+
+(schema
+ reconcellinfo
+ (fields
+ [id :string :unique-identity]
+ [birth :double]
+ [timepoint :ref :many :component]))
+
+(schema reconcellinfo.timepoint (fields [float :double]))
+
+(schema
+ timepoint
+ (fields [id :string :unique-identity] [xyz :ref :component]))
+
+(schema timepoint.xyz (fields [x :double] [y :double] [z :double]))
+
+(schema
+ sequence
+ (fields
+ [id :string :unique-identity]
+ [dna :ref :component]
+ [source-exons :ref :many :component]
+ [overlap-right :ref :component]
+ [overlap-left :ref]
+ [gap-right :ref :many :component]
+ [clone-left-end :ref :many :component]
+ [clone-right-end :ref :many :component]
+ [flipped :boolean]
+ [database :ref :many :component]
+ [protein-id :ref :many :component]
+ [secondary-accession :string :indexed :many]
+ [db-remark :ref :many :component]
+ [keyword :ref :many]
+ [db-annotation :ref :many :component]
+ [embl-dump-info :ref :component]
+ [from-database :ref :component]
+ [from-author :ref :many]
+ [from-laboratory :ref]
+ [genetic-code :ref]
+ [date :ref :many :component]
+ [date-directory :string]
+ [life-stage :ref]
+ [species :ref]
+ [library :ref]
+ [strain :ref]
+ [anatomy-term :ref :many]
+ [analysis :ref]
+ [read-coverage :double]
+ [title :string :indexed]
+ [clone :ref :many]
+ [clone-end-seq-read :ref :many]
+ [go-term :ref :many :component]
+ [paired-read :ref :many]
+ [reference :ref :many :component]
+ [confidential-remark :string :indexed :many]
+ [remark :ref :many :component]
+ [genomic-canonical :boolean]
+ [briggsae-canonical :boolean]
+ [genomic :boolean]
+ [md5 :string]
+ [crc64 :string]
+ [cdna :enum [:tsl-tag :est-5 :cdna-est :capped-5 :est-3] :many]
+ [est-consensus :boolean]
+ [mrna :enum [:processed-mrna :unprocessed-mrna]]
+ [trna :boolean]
+ [rrna :boolean]
+ [snrna :boolean]
+ [snorna :boolean]
+ [scrna :boolean]
+ [mirna :boolean]
+ [ncrna :boolean]
+ [ignore :ref :component]
+ [show-in-reverse-orientation :boolean]
+ [received :instant]
+ [library-construction :instant]
+ [shotgun :instant]
+ [shotgun-complete :instant]
+ [contiguous :instant]
+ [finished :instant]
+ [submitted :instant]
+ [annotated :instant]
+ [archived :ref :component]
+ [match-type :enum [:match-with-function :match-without-function]]
+ [link :boolean]
+ [contains-reads :ref :many]
+ [map :ref :many :component]
+ [interpolated-map-position :ref :component]
+ [oligo :ref :many :component]
+ [assembly-tags :ref :many :component]))
+
+(schema sequence.dna (fields [dna :ref] [length :long]))
+
+(schema sequence.source-exons (fields [start :long] [end :long]))
+
+(schema sequence.overlap-right (fields [sequence :ref] [int :long]))
+
+(schema sequence.gap-right (fields [size :long] [text :string]))
+
+(schema sequence.clone-left-end (fields [clone :ref] [int :long]))
+
+(schema sequence.clone-right-end (fields [clone :ref] [int :long]))
+
+(schema
+ sequence.database
+ (fields [database :ref] [field :ref] [accession :string :indexed]))
+
+(schema
+ sequence.protein-id
+ (fields [sequence :ref] [accession :string] [version :long]))
+
+(schema sequence.db-remark (fields [text :string :indexed]))
+
+(schema sequence.db-annotation (fields [database :ref] [longtext :ref]))
+
+(schema sequence.from-database (fields [database :ref] [version :long]))
+
+(schema sequence.date (fields [datetype :instant] [comment :string]))
+
+(schema sequence.go-term (fields [go-term :ref] [go-code :ref]))
+
+(schema sequence.reference (fields [paper :ref]))
+
+(schema sequence.remark (fields [text :string :indexed]))
+
+(schema sequence.archived (fields [datetype :instant] [disk :string]))
+
+(schema sequence.map (fields [map :ref]))
+
+(schema
+ sequence.interpolated-map-position
+ (fields [map :ref] [float :double]))
+
+(schema
+ sequence.oligo
+ (fields [oligo :ref] [int-b :long] [int-c :long] [method :ref]))
+
+(schema
+ sequence.assembly-tags
+ (fields [type :string] [start :long] [stop :long] [comment :string]))
+
+(schema
+ embl-info
+ (fields
+ [id :string :unique-identity]
+ [location :string]
+ [note :string :many]
+ [product :string :many]))
+
+(schema
+ embl-dump-info
+ (fields
+ [id :string :unique-identity]
+ [embl-dump-method :ref]
+ [id-template :string]
+ [id-division :string]
+ [de-format :string]
+ [os-line :string]
+ [oc-line :string :many]
+ [rl-submission :string :many]
+ [embl-reference :ref :many]
+ [cc-line :string :many]
+ [source-organism :string]
+ [gene-from-name :boolean]))
+
+(schema
+ splice-confirmation
+ (fields
+ [id :string :unique-identity]
+ [cdna :ref :many]
+ [est :ref :many]
+ [ost :ref :many]
+ [rst :ref :many]
+ [rnaseq :ref :many :component]
+ [mass-spec :ref :many]
+ [mrna :ref :many]
+ [homology :string :indexed :many]
+ [utr :ref :many]
+ [false :ref :many]
+ [inconsistent :ref :many]))
+
+(schema splice-confirmation.rnaseq (fields [analysis :ref] [int :long]))
+
+(schema
+ sequence-collection
+ (fields
+ [id :string :unique-identity]
+ [evidence :ref :component]
+ [name :string :indexed :many]
+ [species :ref :many]
+ [strain :ref :many]
+ [laboratory :ref :many]
+ [database :ref :many :component]
+ [first-ws-release :long :many]
+ [latest-ws-release :long :many]
+ [supercedes :ref]
+ [remark :string :indexed :many]
+ [status :ref :component]
+ [sequences :ref :many]))
+
+(schema
+ sequence-collection.database
+ (fields [database :ref] [database-field :ref] [text :string :indexed]))
+
+(schema
+ sequence-collection.status
+ (fields [status :enum [:live :suppressed :dead]]))
+
+(schema
+ cds
+ (fields
+ [id :string :unique-identity]
+ [evidence :ref :component]
+ [source-exons :ref :many :component]
+ [database :ref :many :component]
+ [protein-id :ref :many :component]
+ [db-remark :ref :many :component]
+ [from-laboratory :ref]
+ [species :ref]
+ [genetic-code :ref]
+ [cds :ref :component]
+ [cds-predicted-by :ref :many :component]
+ [prediction-status
+ :enum
+ [:predicted :confirmed :partially-confirmed]]
+ [isoform :ref :component]
+ [start-not-found :long]
+ [end-not-found :boolean]
+ [merge :string :many]
+ [split :string :many]
+ [corresponding-protein :ref :component]
+ [corresponding-pcr-product :ref :many]
+ [matching-cdna :ref :many :component]
+ [go-term :ref :many :component]
+ [reference :ref :many :component]
+ [provisional-description :ref :many :component]
+ [detailed-description :ref :many :component]
+ [concise-description :ref :many :component]
+ [brief-identification :ref :component]
+ [confidential-remark :string :indexed :many]
+ [rnaseq :ref :many :component]
+ [last-reviewed :ref :component]
+ [remark :ref :many :component]))
+
+(schema cds.source-exons (fields [start :long] [end :long]))
+
+(schema
+ cds.database
+ (fields [database :ref] [field :ref] [accession :string :indexed]))
+
+(schema
+ cds.protein-id
+ (fields [sequence :ref] [accession :string] [version :long]))
+
+(schema cds.db-remark (fields [text :string :indexed]))
+
+(schema cds.cds (fields [start :long] [end :long]))
+
+(schema cds.cds-predicted-by (fields [method :ref] [score :double]))
+
+(schema cds.corresponding-protein (fields [protein :ref]))
+
+(schema cds.matching-cdna (fields [sequence :ref]))
+
+(schema cds.go-term (fields [go-term :ref] [go-code :ref]))
+
+(schema cds.reference (fields [paper :ref]))
+
+(schema cds.provisional-description (fields [text :string :indexed]))
+
+(schema cds.detailed-description (fields [text :string :indexed]))
+
+(schema cds.concise-description (fields [text :string :indexed]))
+
+(schema cds.brief-identification (fields [text :string :indexed]))
+
+(schema cds.rnaseq (fields [stage :ref] [fpkm :double]))
+
+(schema cds.last-reviewed (fields [datetype :instant] [person :ref]))
+
+(schema cds.remark (fields [text :string :indexed]))
+
+(schema
+ transcript
+ (fields
+ [id :string :unique-identity]
+ [evidence :ref :component]
+ [source-exons :ref :many :component]
+ [db-remark :ref :many :component]
+ [database :ref :many :component]
+ [from-laboratory :ref]
+ [species :ref]
+ [matching-cdna :ref :many :component]
+ [corresponding-cds :ref :component]
+ [corresponding-pcr-product :ref :many]
+ [reference :ref :many :component]
+ [go-term :ref :many :component]
+ [provisional-description :ref :many :component]
+ [detailed-description :ref :many :component]
+ [concise-description :ref :many :component]
+ [brief-identification :string :indexed]
+ [confidential-remark :string :indexed :many]
+ [rnaseq :ref :many :component]
+ [remark :ref :many :component]
+ [asrna :string]
+ [lincrna :string]
+ [mrna :enum [:processed-mrna :unprocessed-mrna]]
+ [mirna :string]
+ [ncrna :string]
+ [pirna :string]
+ [rrna :string]
+ [scrna :string]
+ [snorna :string]
+ [snrna :string]
+ [snlrna :string]
+ [strna :string]
+ [type :string]
+ [anticodon :string]
+ [isoform :ref :component]
+ [ignore :ref :component]
+ [start-not-found :boolean]
+ [end-not-found :boolean]))
+
+(schema transcript.source-exons (fields [min :long] [max :long]))
+
+(schema transcript.db-remark (fields [text :string :indexed]))
+
+(schema
+ transcript.database
+ (fields [database :ref] [field :ref] [accession :string :indexed]))
+
+(schema transcript.matching-cdna (fields [sequence :ref]))
+
+(schema transcript.corresponding-cds (fields [cds :ref]))
+
+(schema transcript.reference (fields [paper :ref]))
+
+(schema transcript.go-term (fields [go-term :ref] [go-code :ref]))
+
+(schema
+ transcript.provisional-description
+ (fields [text :string :indexed]))
+
+(schema
+ transcript.detailed-description
+ (fields [text :string :indexed]))
+
+(schema transcript.concise-description (fields [text :string :indexed]))
+
+(schema transcript.rnaseq (fields [stage :ref] [fpkm :double]))
+
+(schema transcript.remark (fields [text :string :indexed]))
+
+(schema
+ pseudogene
+ (fields
+ [id :string :unique-identity]
+ [evidence :ref :component]
+ [source-exons :ref :many :component]
+ [db-remark :ref :many :component]
+ [database :ref :many :component]
+ [from-laboratory :ref]
+ [species :ref]
+ [type :ref :component]
+ [transcribed :ref :component]
+ [fragment :ref :component]
+ [processed-pseudogene :ref :component]
+ [unprocessed-pseudogene :ref :component]
+ [truncated-5 :ref :component]
+ [truncated-3 :ref :component]
+ [frameshifts :long]
+ [isoform :ref :component]
+ [matching-cdna :ref :many :component]
+ [brief-identification :ref :component]
+ [corresponding-pcr-product :ref :many]
+ [provisional-description :ref :many :component]
+ [detailed-description :ref :many :component]
+ [concise-description :ref :many :component]
+ [rnaseq :ref :many :component]
+ [last-reviewed :ref :component]
+ [remark :ref :many :component]
+ [confidential-remark :string :indexed :many]))
+
+(schema pseudogene.source-exons (fields [start :long] [end :long]))
+
+(schema pseudogene.db-remark (fields [text :string :indexed]))
+
+(schema
+ pseudogene.database
+ (fields [database :ref] [field :ref] [version :string :indexed]))
+
+(schema
+ pseudogene.type
+ (fields [type :enum [:transposon :coding :rna]]))
+
+(schema pseudogene.matching-cdna (fields [sequence :ref]))
+
+(schema
+ pseudogene.brief-identification
+ (fields [text :string :indexed]))
+
+(schema
+ pseudogene.provisional-description
+ (fields [text :string :indexed]))
+
+(schema
+ pseudogene.detailed-description
+ (fields [text :string :indexed]))
+
+(schema pseudogene.concise-description (fields [text :string :indexed]))
+
+(schema pseudogene.rnaseq (fields [stage :ref] [fpkm :double]))
+
+(schema
+ pseudogene.last-reviewed
+ (fields [datetype :instant] [person :ref]))
+
+(schema pseudogene.remark (fields [text :string :indexed]))
+
+(schema
+ transposon
+ (fields
+ [id :string :unique-identity]
+ [evidence :ref :component]
+ [ltr-region :ref :many :component]
+ [species :ref]
+ [from-laboratory :ref]
+ [member-of :ref :many]
+ [old-name :ref :many :component]
+ [copy-status :ref :component]
+ [corresponding-cds :ref :many :component]
+ [corresponding-pseudogene :ref :many :component]
+ [remark :ref :many :component]))
+
+(schema transposon.ltr-region (fields [start :long] [end :long]))
+
+(schema transposon.old-name (fields [text :string :indexed]))
+
+(schema transposon.copy-status (fields [status :enum [:partial :full]]))
+
+(schema transposon.corresponding-cds (fields [cds :ref]))
+
+(schema transposon.corresponding-pseudogene (fields [pseudogene :ref]))
+
+(schema transposon.remark (fields [text :string :indexed]))
+
+(schema
+ transposon-family
+ (fields
+ [id :string :unique-identity]
+ [evidence :ref :component]
+ [title :string :indexed]
+ [description :string :indexed :many]
+ [remark :ref :many :component]
+ [db-annotation :ref :many :component]
+ [associated-motif :ref :many]))
+
+(schema transposon-family.remark (fields [text :string]))
+
+(schema
+ transposon-family.db-annotation
+ (fields [database :ref] [longtext :ref]))
+
+(schema
+ library
+ (fields
+ [id :string :unique-identity]
+ [database :ref :many :component]
+ [species :ref]
+ [strain :ref]
+ [life-stage :ref]
+ [tissue :string :indexed :many]
+ [description :string :indexed :many]
+ [vector :ref :many]))
+
+(schema
+ library.database
+ (fields [database :ref] [field :ref] [accession :string :indexed]))
+
+(schema
+ homology-group
+ (fields
+ [id :string :unique-identity]
+ [evidence :ref :component]
+ [title :string :indexed :many]
+ [database :ref :many :component]
+ [cog-type :ref :component]
+ [cog-code :ref :component]
+ [eggnog-type :ref :component]
+ [eggnog-code :ref :component]
+ [inparanoid-group :boolean]
+ [orthomcl-group :boolean]
+ [go-term :ref :many]
+ [protein :ref :many]
+ [remark :ref :many :component]))
+
+(schema
+ homology-group.database
+ (fields [database :ref] [database-field :ref] [text :string :indexed]))
+
+(schema homology-group.remark (fields [text :string :indexed]))
+
+(schema
+ cog-codes
+ (fields
+ [id :string :unique-identity]
+ [code-j :boolean]
+ [code-a :boolean]
+ [code-k :boolean]
+ [code-l :boolean]
+ [code-b :boolean]
+ [code-d :boolean]
+ [code-y :boolean]
+ [code-v :boolean]
+ [code-t :boolean]
+ [code-m :boolean]
+ [code-n :boolean]
+ [code-z :boolean]
+ [code-w :boolean]
+ [code-u :boolean]
+ [code-o :boolean]
+ [code-c :boolean]
+ [code-g :boolean]
+ [code-e :boolean]
+ [code-f :boolean]
+ [code-h :boolean]
+ [code-i :boolean]
+ [code-p :boolean]
+ [code-q :boolean]
+ [code-r :boolean]
+ [code-s :boolean]))
+
+(schema
+ homology-type
+ (fields
+ [id :string :unique-identity]
+ [kog :boolean]
+ [twog :boolean]
+ [fog :boolean]
+ [lse :boolean]
+ [nog :boolean]
+ [eunog :boolean]
+ [menog :boolean]
+ [cog :boolean]
+ [nemnog :boolean]))
+
+(schema
+ feature
+ (fields
+ [id :string :unique-identity]
+ [public-name :string :indexed]
+ [other-name :string :indexed :many]
+ [flanking-sequences :ref :component]
+ [mapping-target :ref]
+ [source-location :ref :component]
+ [dna-text :string :indexed]
+ [species :ref]
+ [strain :ref]
+ [merged-into :ref :component]
+ [deprecated :ref :many :component]
+ [description :string :indexed :many]
+ [so-term :ref :many]
+ [defined-by-sequence :ref :many :component]
+ [defined-by-paper :ref :many :component]
+ [defined-by-person :ref :many]
+ [defined-by-analysis :ref :many :component]
+ [score :ref :many :component]
+ [associated-with-gene :ref :many :component]
+ [associated-with-cds :ref :many :component]
+ [associated-with-transcript :ref :many :component]
+ [associated-with-pseudogene :ref :many :component]
+ [associated-with-transposon :ref :many :component]
+ [associated-with-variation :ref :many :component]
+ [associated-with-position-matrix :ref :many :component]
+ [associated-with-operon :ref :many :component]
+ [associated-with-feature :ref :many :component]
+ [associated-with-transcription-factor :ref :many :component]
+ [bound-by-product-of :ref :many :component]
+ [confidential-remark :string :indexed :many]
+ [remark :ref :many :component]))
+
+(schema
+ feature.flanking-sequences
+ (fields [five-prime :string] [three-prime :string]))
+
+(schema
+ feature.source-location
+ (fields [version :long] [sequence :ref] [start :long] [end :long]))
+
+(schema feature.merged-into (fields [feature :ref]))
+
+(schema feature.deprecated (fields [text :string]))
+
+(schema feature.defined-by-sequence (fields [sequence :ref]))
+
+(schema feature.defined-by-paper (fields [paper :ref]))
+
+(schema
+ feature.defined-by-analysis
+ (fields [analysis :ref] [version :long]))
+
+(schema feature.score (fields [float :double] [text :string]))
+
+(schema feature.associated-with-gene (fields [gene :ref]))
+
+(schema feature.associated-with-cds (fields [cds :ref]))
+
+(schema feature.associated-with-transcript (fields [transcript :ref]))
+
+(schema feature.associated-with-pseudogene (fields [pseudogene :ref]))
+
+(schema feature.associated-with-transposon (fields [transposon :ref]))
+
+(schema feature.associated-with-variation (fields [variation :ref]))
+
+(schema
+ feature.associated-with-position-matrix
+ (fields [position-matrix :ref]))
+
+(schema feature.associated-with-operon (fields [operon :ref]))
+
+(schema feature.associated-with-feature (fields [feature :ref]))
+
+(schema
+ feature.associated-with-transcription-factor
+ (fields [transcription-factor :ref]))
+
+(schema feature.bound-by-product-of (fields [gene :ref]))
+
+(schema feature.remark (fields [text :string :indexed]))
+
+(schema
+ transcription-factor
+ (fields
+ [id :string :unique-identity]
+ [name :string]
+ [species :ref]
+ [product-of :ref :many]
+ [associated-with-gene :ref :many :component]
+ [type :ref :many :component]
+ [remark :ref :many :component]))
+
+(schema transcription-factor.associated-with-gene (fields [gene :ref]))
+
+(schema transcription-factor.type (fields [text :string]))
+
+(schema transcription-factor.remark (fields [text :string]))
+
+(schema position-matrix.description (fields [text :string :indexed]))
+
+(schema position-matrix.consensus (fields [text :string]))
+
+(schema position-matrix.bound-by-gene-product (fields [gene :ref]))
+
+(schema
+ position-matrix.transcription-factor
+ (fields [transcription-factor :ref]))
+
+(schema position-matrix.remark (fields [text :string :indexed]))
+
+(schema
+ oligo
+ (fields
+ [id :string :unique-identity]
+ [sequence :string]
+ [length :long]
+ [gc :double]
+ [score :double]
+ [tm :double]
+ [pairwise-scores :ref :many :component]))
+
+(schema
+ oligo.pairwise-scores
+ (fields [oligo :ref] [score :double] [melting-temperature :double]))
+
+(schema
+ genetic-code
+ (fields
+ [id :string :unique-identity]
+ [other-name :string :indexed :many]
+ [ncbi-id :long]
+ [translation :string]
+ [start :string]
+ [stop :string]
+ [base1 :string]
+ [base2 :string]
+ [base3 :string]
+ [remark :string :indexed :many]))
+
+(schema
+ protein
+ (fields
+ [id :string :unique-identity]
+ [peptide :ref :component]
+ [database :ref :many :component]
+ [gene-name :string :indexed :many]
+ [description :string :indexed]
+ [molecular-weight :ref :many :component]
+ [species :ref]
+ [wormpep :boolean]
+ [brigpep :boolean]
+ [history :ref :many :component]
+ [live :boolean]
+ [remark :ref :many :component]))
+
+(schema
+ protein.peptide
+ (fields [peptide :ref] [length :long] [checksum :long]))
+
+(schema
+ protein.database
+ (fields [database :ref] [field :ref] [accession :string :indexed]))
+
+(schema protein.molecular-weight (fields [float :double]))
+
+(schema
+ protein.history
+ (fields [int :long] [text-b :string] [text-c :string :indexed]))
+
+(schema protein.remark (fields [text :string :indexed]))
+
+(schema
+ database-field
+ (fields [id :string :unique-identity] [remark :string :many]))
+
+(schema
+ motif
+ (fields
+ [id :string :unique-identity]
+ [match-sequence :string]
+ [num-mismatch :long]
+ [isoschizomer :ref :many]
+ [offset :long]
+ [cleavage :string]
+ [overhang :long]
+ [company :string]
+ [redundant :boolean]
+ [remark :ref :many :component]
+ [title :string :indexed :many]
+ [database :ref :many :component]
+ [db-remark :ref :many :component]
+ [db-text :ref :many]
+ [substrate :enum [:peptide :dna]]
+ [go-term :ref :many :component]))
+
+(schema motif.remark (fields [text :string :indexed]))
+
+(schema
+ motif.database
+ (fields [database :ref] [field :ref] [accession :string :indexed]))
+
+(schema motif.db-remark (fields [text :string :indexed]))
+
+(schema motif.go-term (fields [go-term :ref] [go-code :ref]))
+
+(schema
+ database
+ (fields
+ [id :string :unique-identity]
+ [name :string :indexed]
+ [description :string]
+ [url :string]
+ [email :string :many]
+ [url-constructor :string]))
+
+(schema
+ method
+ (fields
+ [id :string :unique-identity]
+ [remark :ref :many :component]
+ [no-display :boolean]
+ [frame-sensitive :boolean]
+ [show-up-strand :ref :component]
+ [score-by-offset :boolean]
+ [score-by-width :boolean]
+ [score-by-histogram :double]
+ [score-bounds :ref :component]
+ [percent :boolean]
+ [overlap-mode :enum [:overlap :cluster :bumpable]]
+ [width :double]
+ [symbol :string]
+ [right-priority :double]
+ [max-mag :double]
+ [min-mag :double]
+ [show-text :boolean]
+ [join-blocks :boolean]
+ [display-gaps :boolean]
+ [gapped :boolean]
+ [align-mapping
+ :enum
+ [:allow-clipping :map-gaps :allow-misalign]
+ :many]
+ [blastn :boolean]
+ [blixem :enum [:blixem-x :blixem-p :blixem-n] :many]
+ [belvu :boolean]
+ [embl-feature :string]
+ [embl-threshold :double]
+ [embl-qualifier :ref :many :component]
+ [gene-assemble-method :ref :many :component]
+ [intron-min :long]
+ [exon-min :long]
+ [intron-cost :ref :component]
+ [inter-gene-cost :double]
+ [gf-range :long]
+ [gf-atg-cutoff :double]
+ [gf-5-cutoff :double]
+ [gf-3-cutoff :double]
+ [gff-source :string]
+ [gff-feature :string]
+ [gff-so :ref :component]
+ [embl-dump-info :ref :component]))
+
+(schema method.remark (fields [text :string :indexed]))
+
+(schema method.score-bounds (fields [min :double] [max :double]))
+
+(schema
+ method.embl-qualifier
+ (fields [text-a :string] [text-b :string]))
+
+(schema
+ method.gene-assemble-method
+ (fields [method :ref] [float :double]))
+
+(schema
+ method.intron-cost
+ (fields [bp-cost :double] [log-bp-cost :double] [min :long]))
+
+(schema method.gff-so (fields [so-term :ref] [ace2so :ref]))
+
+(schema
+ reference
+ (fields
+ [id :string :unique-identity]
+ [reference :ref :many]
+ [remark :ref :many :component]
+ [species :ref :many]
+ [description :string :indexed :many]))
+
+(schema reference.remark (fields [text :string :indexed]))
+
+(schema
+ expr-pattern
+ (fields
+ [id :string :unique-identity]
+ [gene :ref :many :component]
+ [reflects-endogenous-expression-of :ref :many]
+ [sequence :ref :many]
+ [clone :ref :many]
+ [protein :ref :many]
+ [protein-description :string :many]
+ [life-stage :ref :many :component]
+ [anatomy-term :ref :many :component]
+ [go-term :ref :many :component]
+ [not-in-life-stage :ref :many :component]
+ [not-in-anatomy-term :ref :many :component]
+ [not-in-go-term :ref :many :component]
+ [subcellular-localization :string :indexed :many]
+ [reporter-gene :string :indexed :many]
+ [in-situ :string :many]
+ [antibody :string :indexed :many]
+ [northern :string :many]
+ [western :string :many]
+ [rt-pcr :string :many]
+ [rnaseq :ref :many]
+ [localizome :string :indexed :many]
+ [microarray :ref :many]
+ [tiling-array :ref :many]
+ [epic :string :indexed :many]
+ [cis-regulatory-element :string :many]
+ [pattern :string :indexed :many]
+ [movieurl :string :many]
+ [species :ref]
+ [remark :ref :many :component]
+ [db-info :ref :many :component]
+ [laboratory :ref :many]
+ [author :ref :many]
+ [date :instant]
+ [strain :ref]
+ [reference :ref :many :component]
+ [transgene :ref :many]
+ [construct :ref :many]
+ [associated-feature :ref :many :component]
+ [antibody-info :ref :many]
+ [curated-by :string]
+ [historical-gene :ref :many :component]))
+
+(schema expr-pattern.gene (fields [gene :ref]))
+
+(schema expr-pattern.life-stage (fields [life-stage :ref]))
+
+(schema expr-pattern.anatomy-term (fields [anatomy-term :ref]))
+
+(schema expr-pattern.go-term (fields [go-term :ref]))
+
+(schema expr-pattern.not-in-life-stage (fields [life-stage :ref]))
+
+(schema expr-pattern.not-in-anatomy-term (fields [anatomy-term :ref]))
+
+(schema expr-pattern.not-in-go-term (fields [go-term :ref]))
+
+(schema expr-pattern.remark (fields [text :string :indexed]))
+
+(schema
+ expr-pattern.db-info
+ (fields [database :ref] [field :ref] [accession :string]))
+
+(schema expr-pattern.reference (fields [paper :ref]))
+
+(schema expr-pattern.associated-feature (fields [feature :ref]))
+
+(schema
+ expr-pattern.historical-gene
+ (fields [gene :ref] [text :string]))
+
+(schema
+ qualifier
+ (fields
+ [id :string :unique-identity]
+ [certain :string :many]
+ [uncertain :string :many]
+ [partial :string :many]
+ [anatomy-term :ref :many]
+ [life-stage :ref :many]))
+
+(schema
+ expr-profile
+ (fields
+ [id :string :unique-identity]
+ [expr-map :ref :many]
+ [reference :ref :many :component]
+ [rnai-result :ref :many]
+ [species :ref]
+ [remark :ref :many :component]))
+
+(schema expr-profile.reference (fields [paper :ref]))
+
+(schema expr-profile.remark (fields [text :string :indexed]))
+
+(schema
+ sk-map
+ (fields
+ [id :string :unique-identity]
+ [x-coord :double]
+ [y-coord :double]
+ [mountain :long]
+ [date :instant]
+ [remark :ref :many :component]))
+
+(schema sk-map.remark (fields [text :string :indexed]))
+
+(schema
+ antibody
+ (fields
+ [id :string :unique-identity]
+ [summary :ref :component]
+ [other-name :string :many]
+ [gene :ref :many :component]
+ [original-publication :ref]
+ [no-original-reference :boolean]
+ [person :ref :many]
+ [location :ref :many]
+ [clonality :enum [:monoclonal :polyclonal]]
+ [antigen :ref :component]
+ [animal :ref :component]
+ [historical-gene :ref :many :component]
+ [possible-pseudonym-of :ref :many]
+ [antibody-for-disease :ref :many :component]
+ [reference :ref :many :component]
+ [remark :ref :many :component]))
+
+(schema antibody.summary (fields [text :string :indexed]))
+
+(schema antibody.gene (fields [gene :ref]))
+
+(schema
+ antibody.antigen
+ (fields
+ [value :enum [:peptide :other-antigen :protein]]
+ [text :string]))
+
+(schema
+ antibody.animal
+ (fields
+ [value
+ :enum
+ [:mouse :chicken :rabbit :rat :other-animal :goat :guinea-pig]]
+ [text :string]))
+
+(schema antibody.historical-gene (fields [gene :ref] [text :string]))
+
+(schema antibody.antibody-for-disease (fields [do-term :ref]))
+
+(schema antibody.reference (fields [paper :ref]))
+
+(schema antibody.remark (fields [text :string :indexed]))
+
+(schema
+ picture
+ (fields
+ [id :string :unique-identity]
+ [description :string :indexed :many]
+ [name :string]
+ [species :ref]
+ [cropped-from :ref :many]
+ [remark :ref :many :component]
+ [expr-pattern :ref :many]
+ [anatomy :ref :many]
+ [cellular-component :ref :many]
+ [wbprocess :ref :many :component]
+ [gene :ref :many]
+ [life-stage :ref :many]
+ [acknowledgement-template :string]
+ [publication-year :string]
+ [article-url :ref :component]
+ [journal-url :ref]
+ [publisher-url :ref]
+ [person-name :string]
+ [reference :ref :many]
+ [contact :ref :many]))
+
+(schema picture.remark (fields [text :string :indexed]))
+
+(schema picture.wbprocess (fields [wbprocess :ref]))
+
+(schema
+ picture.article-url
+ (fields [database :ref] [field :ref] [accession :string :indexed]))
+
+(schema
+ anatomy-term
+ (fields
+ [id :string :unique-identity]
+ [definition :ref :component]
+ [term :ref :component]
+ [synonym :ref :many :component]
+ [embryo-division-time :string :many]
+ [cell-type :string :indexed :many]
+ [program :string :indexed :many]
+ [parent-term :ref]
+ [lineage-name :string :many]
+ [equivalence-origin :ref :many]
+ [herm-origin :ref :many]
+ [male-origin :ref :many]
+ [life-stage :ref :many]
+ [nucleus :ref :many]
+ [contained-in :ref :many]
+ [reconstruction :ref :many :component]
+ [neurodata :ref :many :component]
+ [link-diagram :string :many]
+ [database :ref :many :component]
+ [part-of-p :ref :many]
+ [is-a-p :ref :many]
+ [descendent-of-p :ref :many]
+ [desc-in-herm-p :ref :many]
+ [desc-in-male-p :ref :many]
+ [develops-from-p :ref :many]
+ [cell-p :ref :many]
+ [xunion-of-p :ref :many]
+ [go-term :ref :many :component]
+ [expr-ancestor :ref :many]
+ [expr-descendent :ref :many]
+ [go-ancestor :ref :many]
+ [go-descendent :ref :many]
+ [ancestor :ref :many]
+ [remark :ref :many :component]))
+
+(schema anatomy-term.definition (fields [text :string :indexed]))
+
+(schema anatomy-term.term (fields [text :string :indexed]))
+
+(schema anatomy-term.synonym (fields [text :string :indexed]))
+
+(schema anatomy-term.reconstruction (fields [reconstruction :ref]))
+
+(schema anatomy-term.neurodata (fields [anatomy-term :ref]))
+
+(schema
+ anatomy-term.database
+ (fields [database :ref] [field :ref] [accession :string :indexed]))
+
+(schema anatomy-term.go-term (fields [go-term :ref] [ao-code :ref]))
+
+(schema anatomy-term.remark (fields [text :string :indexed]))
+
+(schema
+ anatomy-function
+ (fields
+ [id :string :unique-identity]
+ [assay :ref :many :component]
+ [phenotype :ref :component]
+ [gene :ref :component]
+ [involved :ref :many :component]
+ [not-involved :ref :many :component]
+ [remark :ref :many :component]
+ [reference :ref]))
+
+(schema anatomy-function.assay (fields [ao-code :ref] [condition :ref]))
+
+(schema anatomy-function.phenotype (fields [phenotype :ref]))
+
+(schema anatomy-function.gene (fields [gene :ref]))
+
+(schema anatomy-function.involved (fields [anatomy-term :ref]))
+
+(schema anatomy-function.not-involved (fields [anatomy-term :ref]))
+
+(schema anatomy-function.remark (fields [text :string]))
+
+(schema
+ anatomy-function-info
+ (fields
+ [id :string :unique-identity]
+ [autonomous :string :many]
+ [nonautonomous :string :many]
+ [sufficient :string :many]
+ [insufficient :string :many]
+ [necessary :string :many]
+ [unnecessary :string :many]
+ [remark :string :many]))
+
+(schema
+ life-stage
+ (fields
+ [id :string :unique-identity]
+ [anatomy-term :ref :many]
+ [contained-in :ref :many]
+ [preceded-by :ref :many]
+ [remark :ref :many :component]
+ [definition :string :indexed :many]
+ [public-name :string :indexed]
+ [other-name :string :indexed :many]
+ [reference :ref :many :component]
+ [curated-by :string]))
+
+(schema life-stage.remark (fields [text :string :indexed]))
+
+(schema life-stage.reference (fields [paper :ref]))
+
+(schema
+ tree
+ (fields
+ [id :string :unique-identity]
+ [description :string :indexed]
+ [type :enum [:protein :dna :cell-lineage :taxonomy]]
+ [root :ref]
+ [no-header :boolean]
+ [descriptive-labels :boolean]
+ [colour :boolean]
+ [normalization :double]
+ [bootstrap-factor :double]
+ [hide-bootstraps :boolean]
+ [alignment :enum [:middle :top :unrooted :bottom]]
+ [embedded-tree :ref :many]))
+
+(schema
+ treenode
+ (fields
+ [id :string :unique-identity]
+ [label :string :indexed]
+ [xid :long]
+ [description :string :indexed :many]
+ [type :enum [:interior :root :leaf]]
+ [distance :double]
+ [bootstrap :double]
+ [tree :ref]
+ [parent :ref]
+ [hide :boolean]
+ [colour :ref :component]
+ [hide-bootstraps :boolean]
+ [show-bootstrap :boolean]
+ [taxon :boolean]
+ [anatomy-term :ref]
+ [embedded-tree :ref :many]))
+
+(schema
+ transgene
+ (fields
+ [id :string :unique-identity]
+ [evidence :ref :component]
+ [public-name :string :indexed]
+ [summary :ref :component]
+ [synonym :string :indexed :many]
+ [coinjection-other :string :indexed :many]
+ [integration-method :string :indexed]
+ [integrated-from :ref :many]
+ [laboratory :ref :many :component]
+ [author :ref :many]
+ [construction-summary :string :indexed :many]
+ [extrachromosomal :boolean]
+ [integrated :boolean]
+ [map :ref :many :component]
+ [map-evidence :ref :component]
+ [mapping-data :enum [:multi-point] :many]
+ [phenotype :ref :many :component]
+ [phenotype-not-observed :ref :many :component]
+ [marker-for :ref :many :component]
+ [strain :ref :many]
+ [transgene-for-disease :ref :many :component]
+ [reference :ref :many :component]
+ [species :ref]
+ [remark :ref :many :component]))
+
+(schema transgene.summary (fields [text :string :indexed]))
+
+(schema transgene.laboratory (fields [laboratory :ref]))
+
+(schema transgene.map (fields [map :ref]))
+
+(schema transgene.phenotype (fields [phenotype :ref]))
+
+(schema transgene.phenotype-not-observed (fields [phenotype :ref]))
+
+(schema transgene.marker-for (fields [text :string :indexed]))
+
+(schema transgene.transgene-for-disease (fields [do-term :ref]))
+
+(schema transgene.reference (fields [paper :ref]))
+
+(schema transgene.remark (fields [text :string :indexed]))
+
+(schema
+ construct
+ (fields
+ [id :string :unique-identity]
+ [evidence :ref :component]
+ [public-name :string :indexed :many]
+ [other-name :string :indexed :many]
+ [summary :ref :component]
+ [database :ref :many :component]
+ [sequence-feature :ref :many]
+ [driven-by-gene :ref :many :component]
+ [gene :ref :many :component]
+ [three-prime-utr :ref :many :component]
+ [fusion-reporter :string :indexed :many]
+ [other-reporter :string :indexed :many]
+ [purification-tag :string :indexed :many]
+ [recombinant-site :string :indexed :many]
+ [type-of-construct :string :indexed :many]
+ [selection-marker :string :indexed :many]
+ [construction-summary :string :indexed :many]
+ [dna-text :string :many]
+ [clone :ref :many]
+ [transgene-construct :ref :many]
+ [transgene-coinjection :ref :many]
+ [construct-for-disease :ref :many :component]
+ [reference :ref :many]
+ [person :ref :many]
+ [laboratory :ref :many :component]
+ [historical-gene :ref :many :component]
+ [remark :ref :many :component]))
+
+(schema construct.summary (fields [text :string :indexed]))
+
+(schema
+ construct.database
+ (fields [database :ref] [field :ref] [accession :string :indexed]))
+
+(schema construct.driven-by-gene (fields [gene :ref]))
+
+(schema construct.gene (fields [gene :ref]))
+
+(schema construct.three-prime-utr (fields [gene :ref]))
+
+(schema construct.construct-for-disease (fields [do-term :ref]))
+
+(schema construct.laboratory (fields [laboratory :ref]))
+
+(schema construct.historical-gene (fields [gene :ref] [text :string]))
+
+(schema construct.remark (fields [text :string :indexed]))
+
+(schema
+ rnai
+ (fields
+ [id :string :unique-identity]
+ [evidence :ref :component]
+ [history-name :string :indexed]
+ [dna-text :ref :many :component]
+ [sequence :ref :many]
+ [clone :ref :many]
+ [pcr-product :ref :many]
+ [uniquely-mapped :boolean]
+ [laboratory :ref :many]
+ [date :instant]
+ [strain :ref]
+ [genotype :string :indexed]
+ [treatment :string :indexed]
+ [life-stage :ref]
+ [temperature :long]
+ [delivered-by
+ :enum
+ [:soaking :bacterial-feeding :injection :transgene-expression]]
+ [predicted-gene :ref :many :component]
+ [gene :ref :many :component]
+ [transcript :ref :many :component]
+ [pseudogene :ref :many :component]
+ [database :ref :many :component]
+ [species :ref]
+ [reference :ref :component]
+ [phenotype :ref :many :component]
+ [phenotype-not-observed :ref :many :component]
+ [remark :ref :many :component]))
+
+(schema rnai.dna-text (fields [sequence :string] [name :string]))
+
+(schema rnai.predicted-gene (fields [cds :ref]))
+
+(schema rnai.gene (fields [gene :ref]))
+
+(schema rnai.transcript (fields [transcript :ref]))
+
+(schema rnai.pseudogene (fields [pseudogene :ref]))
+
+(schema
+ rnai.database
+ (fields [database :ref] [field :ref] [accession :string :indexed]))
+
+(schema rnai.reference (fields [paper :ref]))
+
+(schema rnai.phenotype (fields [phenotype :ref]))
+
+(schema rnai.phenotype-not-observed (fields [phenotype :ref]))
+
+(schema rnai.remark (fields [text :string :indexed]))
+
+(schema
+ phenotype-info
+ (fields
+ [id :string :unique-identity]
+ [paper-evidence :ref :many]
+ [person-evidence :ref :many]
+ [curator-confirmed :ref :many]
+ [remark :ref :many :component]
+ [quantity-description :ref :many :component]
+ [quantity :ref :component]
+ [incomplete :ref :many :component]
+ [low :ref :many :component]
+ [high :ref :many :component]
+ [complete :ref :many :component]
+ [range :ref :component]
+ [recessive :ref :component]
+ [semi-dominant :ref :component]
+ [dominant :ref :component]
+ [haplo-insufficient :ref :component]
+ [caused-by-gene :ref :many :component]
+ [caused-by-other :ref :many :component]
+ [rescued-by-transgene :ref :many]
+ [variation-effect :ref :many :component]
+ [molecule :ref :many :component]
+ [pathogen :ref :many :component]
+ [anatomy-term :ref :many :component]
+ [life-stage :ref :many :component]
+ [go-term :ref :many :component]
+ [molecule-affected :ref :many :component]
+ [heat-sensitive :ref :many :component]
+ [cold-sensitive :ref :many :component]
+ [maternal :ref :component]
+ [paternal :ref :component]
+ [strain :ref :many :component]
+ [treatment :ref :many :component]
+ [temperature :ref :many :component]
+ [genotype :ref :many :component]
+ [ease-of-scoring :ref :component]))
+
+(schema phenotype-info.remark (fields [text :string :indexed]))
+
+(schema
+ phenotype-info.quantity-description
+ (fields [text :string :indexed]))
+
+(schema phenotype-info.quantity (fields [int-a :long] [int-b :long]))
+
+(schema phenotype-info.incomplete (fields [text :string]))
+
+(schema phenotype-info.low (fields [text :string]))
+
+(schema phenotype-info.high (fields [text :string]))
+
+(schema phenotype-info.complete (fields [text :string]))
+
+(schema phenotype-info.range (fields [int-a :long] [int-b :long]))
+
+(schema phenotype-info.caused-by-gene (fields [gene :ref]))
+
+(schema phenotype-info.caused-by-other (fields [text :string :indexed]))
+
+(schema
+ phenotype-info.variation-effect
+ (fields
+ [value
+ :enum
+ [:loss-of-function-undetermined-extent
+ :hypermorph-gain-of-function
+ :dominant-negative-gain-of-function
+ :predicted-hypomorph-via-sequence
+ :neomorph-gain-of-function
+ :predicted-null-via-sequence
+ :hypomorph-reduction-of-function
+ :null
+ :wild-allele
+ :antimorph-gain-of-function
+ :probable-null-via-phenotype
+ :gain-of-function-undetermined-type
+ :probable-hypomorph-via-phenotype]]))
+
+(schema phenotype-info.molecule (fields [molecule :ref]))
+
+(schema phenotype-info.pathogen (fields [species :ref]))
+
+(schema
+ phenotype-info.anatomy-term
+ (fields [anatomy-term :ref] [pato-term :ref]))
+
+(schema
+ phenotype-info.life-stage
+ (fields [life-stage :ref] [pato-term :ref]))
+
+(schema phenotype-info.go-term (fields [go-term :ref] [pato-term :ref]))
+
+(schema
+ phenotype-info.molecule-affected
+ (fields [molecule :ref] [pato-term :ref]))
+
+(schema phenotype-info.heat-sensitive (fields [text :string]))
+
+(schema phenotype-info.cold-sensitive (fields [text :string]))
+
+(schema
+ phenotype-info.maternal
+ (fields [value :enum [:with-maternal-effect :strictly-maternal]]))
+
+(schema phenotype-info.strain (fields [strain :ref]))
+
+(schema phenotype-info.treatment (fields [text :string :indexed]))
+
+(schema phenotype-info.temperature (fields [text :string :indexed]))
+
+(schema phenotype-info.genotype (fields [text :string :indexed]))
+
+(schema
+ phenotype-info.ease-of-scoring
+ (fields
+ [value
+ :enum
+ [:es3-easy-to-score
+ :es2-difficult-to-score
+ :es1-very-hard-to-score
+ :es0-impossible-to-score]]))
+
+(schema
+ pcr-product
+ (fields
+ [id :string :unique-identity]
+ [left-mapping-primer :string]
+ [right-mapping-primer :string]
+ [species :ref]
+ [oligo :ref :many :component]
+ [assay-conditions :ref :many]
+ [from-laboratory :ref]
+ [amplified :long :many]
+ [clone :ref :many]
+ [remark :ref :many :component]))
+
+(schema
+ pcr-product.oligo
+ (fields [oligo :ref] [int-b :long] [int-c :long]))
+
+(schema pcr-product.remark (fields [text :string :indexed]))
+
+(schema
+ phenotype
+ (fields
+ [id :string :unique-identity]
+ [description :ref :component]
+ [primary-name :ref :component]
+ [synonym :ref :many :component]
+ [short-name :ref :many :component]
+ [assay :ref :component]
+ [remark :ref :many :component]
+ [specialisation-of :ref :many]
+ [dead :boolean]
+ [go-term :ref :many :component]
+ [do-term :ref :many :component]))
+
+(schema phenotype.description (fields [text :string :indexed]))
+
+(schema phenotype.primary-name (fields [text :string :indexed]))
+
+(schema phenotype.synonym (fields [text :string :indexed]))
+
+(schema phenotype.short-name (fields [text :string :indexed]))
+
+(schema phenotype.assay (fields [text :string :indexed]))
+
+(schema phenotype.remark (fields [text :string :indexed]))
+
+(schema phenotype.go-term (fields [go-term :ref] [go-code :ref]))
+
+(schema phenotype.do-term (fields [do-term :ref]))
+
+(schema
+ operon
+ (fields
+ [id :string :unique-identity]
+ [public-name :string :indexed]
+ [species :ref]
+ [contains-gene :ref :many :component]
+ [reference :ref :many :component]
+ [description :ref :component]
+ [merged-into :ref :component]
+ [split-into :ref :many :component]
+ [deprecated :ref :many :component]
+ [remark :ref :many :component]))
+
+(schema operon.contains-gene (fields [gene :ref]))
+
+(schema operon.reference (fields [paper :ref]))
+
+(schema operon.description (fields [text :string :indexed]))
+
+(schema operon.merged-into (fields [operon :ref]))
+
+(schema operon.split-into (fields [operon :ref]))
+
+(schema operon.deprecated (fields [text :string]))
+
+(schema operon.remark (fields [text :string]))
+
+(schema
+ trans-splice-leader
+ (fields
+ [id :string :unique-identity]
+ [sl1 :ref :component]
+ [sl2 :ref :component]
+ [microarray :ref :component]
+ [inferred :ref :component]))
+
+(schema
+ movie
+ (fields
+ [id :string :unique-identity]
+ [description :string :indexed :many]
+ [public-name :string]
+ [reference :ref :many]
+ [db-info :ref :many :component]
+ [rnai :ref :many]
+ [variation :ref :many :component]
+ [expr-pattern :ref :many]
+ [remark :ref :many :component]))
+
+(schema
+ movie.db-info
+ (fields [database :ref] [field :ref] [accession :string]))
+
+(schema movie.variation (fields [variation :ref]))
+
+(schema movie.remark (fields [text :string :indexed]))
+
+(schema
+ microarray
+ (fields
+ [id :string :unique-identity]
+ [chip-type :string :indexed]
+ [chip-info :string :indexed :many]
+ [reference :ref :many]
+ [url :string :many]
+ [remark :ref :many :component]))
+
+(schema microarray.remark (fields [text :string :indexed]))
+
+(schema
+ microarray-results
+ (fields
+ [id :string :unique-identity]
+ [species :ref]
+ [pcr-product :ref]
+ [oligo-set :ref]
+ [gene :ref :many :component]
+ [cds :ref :many :component]
+ [transcript :ref :many :component]
+ [pseudogene :ref :many :component]
+ [microarray :ref :many]
+ [results :ref :many :component]
+ [expr-pattern :ref :many]
+ [min :ref :component]
+ [max :ref :component]
+ [remark :ref :many :component]))
+
+(schema microarray-results.gene (fields [gene :ref]))
+
+(schema microarray-results.cds (fields [cds :ref]))
+
+(schema microarray-results.transcript (fields [transcript :ref]))
+
+(schema microarray-results.pseudogene (fields [pseudogene :ref]))
+
+(schema
+ microarray-results.results
+ (fields [microarray-experiment :ref]))
+
+(schema
+ microarray-results.min
+ (fields [value :double] [experiment :ref]))
+
+(schema
+ microarray-results.max
+ (fields [value :double] [experiment :ref]))
+
+(schema microarray-results.remark (fields [text :string :indexed]))
+
+(schema
+ microarray-data
+ (fields
+ [id :string :unique-identity]
+ [a-vs-b-log-ratio :double]
+ [a-vs-b-sd :double]
+ [frequency :double]
+ [number-of-experiments :long]
+ [range-within-paper :ref :component]
+ [confidence-level :double]
+ [p-value :double]
+ [presence :enum [:pa :np :ps]]
+ [remark :ref :many :component]))
+
+(schema
+ microarray-data.range-within-paper
+ (fields [min :double] [max :double]))
+
+(schema microarray-data.remark (fields [text :string]))
+
+(schema
+ microarray-experiment
+ (fields
+ [id :string :unique-identity]
+ [microarray :ref :many]
+ [species :ref]
+ [sample-a :ref]
+ [sample-b :ref]
+ [microarray-sample :ref]
+ [reference :ref :many]
+ [remark :ref :many :component]))
+
+(schema microarray-experiment.remark (fields [text :string]))
+
+(schema
+ oligo-set
+ (fields
+ [id :string :unique-identity]
+ [species :ref]
+ [target-exons :ref :many :component]
+ [oligo :ref :many]
+ [overlaps-cds :ref :many :component]
+ [overlaps-transcript :ref :many :component]
+ [overlaps-pseudogene :ref :many :component]
+ [remark :ref :many :component]
+ [type
+ :enum
+ [:agilent-microarray-probe
+ :washu-gsc-microarray-probe
+ :affymetrix-microarray-probe
+ :affymetrix-tiling-array-probe]
+ :many]))
+
+(schema oligo-set.target-exons (fields [start :long] [end :long]))
+
+(schema oligo-set.overlaps-cds (fields [cds :ref]))
+
+(schema oligo-set.overlaps-transcript (fields [transcript :ref]))
+
+(schema oligo-set.overlaps-pseudogene (fields [pseudogene :ref]))
+
+(schema oligo-set.remark (fields [text :string]))
+
+(schema
+ expression-cluster
+ (fields
+ [id :string :unique-identity]
+ [description :string :indexed :many]
+ [species :ref]
+ [algorithm :string :many]
+ [reference :ref :many :component]
+ [based-on-wb-release :long :many]
+ [microarray-results :ref :many :component]
+ [sage-tag :ref :many :component]
+ [gene :ref :many :component]
+ [microarray-experiment :ref :many]
+ [mass-spectrometry :ref :many]
+ [rnaseq :ref :many]
+ [tiling-array :ref :many]
+ [qpcr :ref :many]
+ [expr-pattern :ref :many :component]
+ [regulated-by-gene :ref :many]
+ [regulated-by-treatment :string :many]
+ [regulated-by-molecule :ref :many]
+ [life-stage :ref :many]
+ [go-term :ref :many]
+ [anatomy-term :ref :many :component]
+ [remark :ref :many :component]))
+
+(schema expression-cluster.reference (fields [paper :ref]))
+
+(schema
+ expression-cluster.microarray-results
+ (fields [microarray-results :ref] [text :string]))
+
+(schema
+ expression-cluster.sage-tag
+ (fields [sage-tag :ref] [text :string]))
+
+(schema expression-cluster.gene (fields [gene :ref] [text :string]))
+
+(schema expression-cluster.expr-pattern (fields [expr-pattern :ref]))
+
+(schema expression-cluster.anatomy-term (fields [anatomy-term :ref]))
+
+(schema expression-cluster.remark (fields [text :string :indexed]))
+
+(schema
+ expression-cluster-info
+ (fields
+ [id :string :unique-identity]
+ [expressed :boolean]
+ [depleted :boolean]
+ [enriched :boolean]
+ [dissection :boolean]
+ [mrna-tagging :boolean]
+ [facs :boolean]))
+
+(schema
+ sage-tag
+ (fields
+ [id :string :unique-identity]
+ [evidence :ref :component]
+ [tag-sequence :string]
+ [anchoring-enzyme :ref]
+ [tag-length :long]
+ [most-three-prime :boolean]
+ [unambiguously-mapped :boolean]
+ [predicted-cds :ref :many :component]
+ [gene :ref :many :component]
+ [transcript :ref :many :component]
+ [pseudogene :ref :many :component]
+ [results :ref :many :component]
+ [remark :ref :many :component]))
+
+(schema sage-tag.predicted-cds (fields [cds :ref]))
+
+(schema sage-tag.gene (fields [gene :ref]))
+
+(schema sage-tag.transcript (fields [transcript :ref]))
+
+(schema sage-tag.pseudogene (fields [pseudogene :ref]))
+
+(schema sage-tag.results (fields [sage-experiment :ref]))
+
+(schema sage-tag.remark (fields [text :string :indexed]))
+
+(schema
+ sage-mapping-info
+ (fields
+ [id :string :unique-identity]
+ [transcript-source :string :indexed]
+ [position :long]
+ [strand :enum [:antisense :sense]]
+ [most-three-prime :boolean]
+ [unambiguously-mapped :boolean]))
+
+(schema
+ sage-data
+ (fields
+ [id :string :unique-identity]
+ [frequency :long]
+ [total-tag-count :long]
+ [relative-abundance :double]
+ [significance :double]
+ [confidence-level :double]
+ [standard-deviation :double]
+ [number-of-experiments :long]
+ [sequence-quality :double]))
+
+(schema
+ sage-experiment
+ (fields
+ [id :string :unique-identity]
+ [sample :ref]
+ [species :ref]
+ [reference :ref :many]
+ [remark :ref :many :component]))
+
+(schema sage-experiment.remark (fields [text :string :indexed]))
+
+(schema
+ person
+ (fields
+ [id :string :unique-identity]
+ [postgresql-id :string]
+ [database :ref :many :component]
+ [first-name :string :indexed]
+ [middle-name :string :indexed :many]
+ [last-name :string :indexed]
+ [standard-name :string :indexed]
+ [full-name :string :indexed]
+ [also-known-as :string :indexed :many]
+ [principal-investigator :boolean]
+ [affiliation :string :many]
+ [address :ref :component]
+ [last-verified :instant]
+ [last-attempt-to-contact :ref :component]
+ [old-address :ref :many :component]
+ [left-the-field :string :many]
+ [merged-into :ref]
+ [status :enum [:valid :invalid] :many]
+ [comment :string :many]
+ [supervised-by :ref :many :component]
+ [worked-with :ref :many :component]
+ [publishes-as :ref :many]
+ [possibly-publishes-as :ref :many]))
+
+(schema
+ person.database
+ (fields [database :ref] [field :ref] [accession :string :indexed]))
+
+(schema
+ person.last-attempt-to-contact
+ (fields [date :instant] [note :string]))
+
+(schema person.old-address (fields [datetype :instant]))
+
+(schema person.supervised-by (fields [person :ref]))
+
+(schema person.worked-with (fields [person :ref]))
+
+(schema
+ address
+ (fields
+ [id :string :unique-identity]
+ [street-address :string :many]
+ [country :string]
+ [institution :boolean]
+ [email :string :many]
+ [main-phone :string :many]
+ [lab-phone :string :many]
+ [office-phone :string :many]
+ [other-phone :string :many]
+ [fax :string :many]
+ [web-page :string :many]))
+
+(schema
+ role
+ (fields
+ [id :string :unique-identity]
+ [assistant-professor :ref :many :component]
+ [phd :ref :many :component]
+ [postdoc :ref :many :component]
+ [masters :ref :many :component]
+ [undergrad :ref :many :component]
+ [highschool :ref :many :component]
+ [sabbatical :ref :many :component]
+ [lab-visitor :ref :many :component]
+ [collaborated :ref :many :component]
+ [research-staff :ref :many :component]
+ [unknown :ref :many :component]))
+
+(schema role.assistant-professor (fields [from :instant] [to :instant]))
+
+(schema role.phd (fields [from :instant] [to :instant]))
+
+(schema role.postdoc (fields [from :instant] [to :instant]))
+
+(schema role.masters (fields [from :instant] [to :instant]))
+
+(schema role.undergrad (fields [from :instant] [to :instant]))
+
+(schema role.highschool (fields [from :instant] [to :instant]))
+
+(schema role.sabbatical (fields [from :instant] [to :instant]))
+
+(schema role.lab-visitor (fields [from :instant] [to :instant]))
+
+(schema role.collaborated (fields [from :instant] [to :instant]))
+
+(schema role.research-staff (fields [from :instant] [to :instant]))
+
+(schema role.unknown (fields [from :instant] [to :instant]))
+
+(schema
+ author
+ (fields
+ [id :string :unique-identity]
+ [full-name :string :many]
+ [also-known-as :string :many]
+ [old-lab :ref :many]
+ [mail :string :many]
+ [e-mail :string :many]
+ [phone :string :many]
+ [fax :string :many]
+ [paper :ref :many]
+ [keyword :ref :many]))
+
+(schema
+ paper
+ (fields
+ [id :string :unique-identity]
+ [name :string :indexed :many]
+ [database :ref :many :component]
+ [merged-into :ref]
+ [status :enum [:valid :invalid] :many]
+ [erratum-for :ref :many]
+ [title :string :indexed]
+ [journal :string :indexed]
+ [publisher :string]
+ [editor :string :indexed :many]
+ [page :string]
+ [volume :string]
+ [publication-date :string :indexed]
+ [contained-in :ref :many]
+ [author :ref :many :component]
+ [person :ref :many :component]
+ [not-person :ref :many :component]
+ [affiliation :string :many]
+ [brief-citation :string]
+ [abstract :ref :many]
+ [url :string :many]
+ [type :ref :many :component]
+ [species :ref :many :component]
+ [go-term :ref :many]
+ [curation-pipeline :enum [:phenotype2go] :many]
+ [keyword :string :indexed :many]
+ [remark :ref :many :component]))
+
+(schema
+ paper.database
+ (fields [database :ref] [field :ref] [accession :string :indexed]))
+
+(schema paper.author (fields [author :ref]))
+
+(schema paper.person (fields [person :ref]))
+
+(schema paper.not-person (fields [person :ref]))
+
+(schema
+ paper.type
+ (fields
+ [type
+ :enum
+ [:technical-report
+ :news
+ :editorial
+ :historical-article
+ :congresses
+ :retracted-publication
+ :gazette-article
+ :book
+ :lectures
+ :published-erratum
+ :biography
+ :wormbook
+ :retraction-of-publication
+ :letter
+ :book-chapter
+ :monograph
+ :interactive-tutorial
+ :journal-article
+ :meeting-abstract
+ :review
+ :email
+ :comment
+ :interview
+ :other]]))
+
+(schema paper.species (fields [species :ref]))
+
+(schema paper.remark (fields [text :string :indexed]))
+
+(schema
+ affiliation
+ (fields
+ [id :string :unique-identity]
+ [affiliation-address :string]
+ [person :ref :many]))
+
+(schema
+ laboratory
+ (fields
+ [id :string :unique-identity]
+ [mail :string :many]
+ [phone :string :many]
+ [e-mail :string :many]
+ [fax :string :many]
+ [url :string :many]
+ [clean-address :ref :component]
+ [representative :ref :many]
+ [strain-designation :string]
+ [allele-designation :string]
+ [alleles :ref :many]
+ [registered-lab-members :ref :many]
+ [past-lab-members :ref :many]
+ [remark :ref :many :component]))
+
+(schema laboratory.remark (fields [text :string :indexed]))
+
+(schema
+ gr-condition
+ (fields
+ [id :string :unique-identity]
+ [life-stage :ref :many]
+ [anatomy-term :ref :many]
+ [subcellular-localization :string :indexed :many]))
+
+(schema
+ variation
+ (fields
+ [id :string :unique-identity]
+ [evidence :ref :component]
+ [public-name :string :indexed]
+ [other-name :string :indexed :many]
+ [flanking-sequences :ref :component]
+ [mapping-target :ref]
+ [source-location :ref :component]
+ [cgh-deleted-probes :ref :component]
+ [text :enum [:text]]
+ [substitution :ref :component]
+ [insertion :ref :component]
+ [deletion :ref :component]
+ [tandem-duplication :ref :component]
+ [pcr-product :ref :many]
+ [seqstatus :enum [:not-sequenced :sequenced :pending-curation]]
+ [deletion-verification :ref :many :component]
+ [engineered-allele :boolean]
+ [allele :boolean]
+ [snp :boolean]
+ [confirmed-snp :boolean]
+ [predicted-snp :boolean]
+ [reference-strain-digest :ref :many :component]
+ [polymorphic-strain-digest :ref :many :component]
+ [transposon-insertion :ref :many]
+ [natural-variant :boolean]
+ [species :ref]
+ [strain :ref :many :component]
+ [laboratory :ref :many]
+ [author :ref :many]
+ [person :ref :many]
+ [analysis :ref :many]
+ [corresponding-transgene :ref]
+ [production-method
+ :enum
+ [:talens
+ :zfnhr-repair
+ :mossci
+ :mosdel
+ :crispr-cas9
+ :nhej
+ :homologous-recombination
+ :zfnnhej-repair]
+ :many]
+ [expr-pattern :ref :many :component]
+ [database :ref :many :component]
+ [ko-consortium-allele :boolean]
+ [nbp-allele :boolean]
+ [nemagenetag-consortium-allele :boolean]
+ [detection-method :string :many]
+ [nature-of-variation :enum [:synthetic :polymorphic]]
+ [merged-into :ref]
+ [split-into :ref :many]
+ [status :ref :component]
+ [linked-to :ref :many]
+ [gene :ref :many :component]
+ [predicted-cds :ref :many :component]
+ [transcript :ref :many :component]
+ [pseudogene :ref :many :component]
+ [possibly-affects :ref :many :component]
+ [date :instant :many]
+ [mutagen :ref :component]
+ [forward-genetics :ref :many :component]
+ [reverse-genetics :ref :many :component]
+ [transposon-excision :ref :many]
+ [derived-from-variation :ref :many]
+ [derived-from-construct :ref :many]
+ [gene-class :ref :many]
+ [male-mating-efficiency :ref :component]
+ [hermaphrodite-mating-efficiency :ref :component]
+ [map :ref :many :component]
+ [interpolated-map-position :ref :component]
+ [phenotype :ref :many :component]
+ [phenotype-remark :ref :many :component]
+ [phenotype-not-observed :ref :many :component]
+ [reference :ref :many :component]
+ [remark :ref :many :component]))
+
+(schema
+ variation.flanking-sequences
+ (fields [five-prime :string] [three-prime :string]))
+
+(schema
+ variation.source-location
+ (fields [version :long] [sequence :ref] [start :long] [end :long]))
+
+(schema
+ variation.cgh-deleted-probes
+ (fields [text-a :string] [text-b :string]))
+
+(schema variation.substitution (fields [ref :string] [alt :string]))
+
+(schema variation.insertion (fields [text :string]))
+
+(schema variation.deletion (fields [text :string]))
+
+(schema variation.deletion-verification (fields [text :string]))
+
+(schema
+ variation.reference-strain-digest
+ (fields [site :string] [enzyme :string] [band-size :string]))
+
+(schema
+ variation.polymorphic-strain-digest
+ (fields [site :string] [enzyme :string] [band-size :string]))
+
+(schema variation.strain (fields [strain :ref]))
+
+(schema variation.expr-pattern (fields [expr-pattern :ref]))
+
+(schema
+ variation.database
+ (fields [database :ref] [field :ref] [accession :string :indexed]))
+
+(schema
+ variation.status
+ (fields [value :enum [:live :suppressed :dead]]))
+
+(schema variation.gene (fields [gene :ref]))
+
+(schema variation.predicted-cds (fields [cds :ref]))
+
+(schema variation.transcript (fields [transcript :ref]))
+
+(schema variation.pseudogene (fields [pseudogene :ref]))
+
+(schema variation.possibly-affects (fields [gene :ref]))
+
+(schema variation.mutagen (fields [text :string]))
+
+(schema variation.forward-genetics (fields [text :string]))
+
+(schema variation.reverse-genetics (fields [text :string]))
+
+(schema
+ variation.male-mating-efficiency
+ (fields
+ [value
+ :enum
+ [:me3-mating-always-successful
+ :me0-mating-not-successful
+ :me2-mating-usually-successful
+ :me1-mating-rarely-successful]]))
+
+(schema
+ variation.hermaphrodite-mating-efficiency
+ (fields
+ [value
+ :enum
+ [:hme3-mating-always-successful
+ :hme0-mating-not-successful
+ :hme2-mating-usually-successful
+ :hme1-mating-rarely-successful]]))
+
+(schema variation.map (fields [map :ref]))
+
+(schema
+ variation.interpolated-map-position
+ (fields [map :ref] [position :double]))
+
+(schema variation.phenotype (fields [phenotype :ref]))
+
+(schema variation.phenotype-remark (fields [text :string :indexed]))
+
+(schema variation.phenotype-not-observed (fields [phenotype :ref]))
+
+(schema variation.reference (fields [paper :ref]))
+
+(schema variation.remark (fields [text :string :indexed]))
+
+(schema
+ molecular-change
+ (fields
+ [id :string :unique-identity]
+ [missense :ref :many :component]
+ [silent :ref :many :component]
+ [nonsense :ref :component]
+ [splice-site :ref :component]
+ [frameshift :ref :many :component]
+ [readthrough :ref :many :component]
+ [intron :ref :component]
+ [coding-exon :ref :component]
+ [noncoding-exon :ref :component]
+ [promoter :ref :component]
+ [utr-3 :ref :component]
+ [utr-5 :ref :component]
+ [regulatory-feature :ref :component]
+ [genomic-neighbourhood :ref :component]))
+
+(schema molecular-change.missense (fields [int :long] [text :string]))
+
+(schema molecular-change.silent (fields [text :string]))
+
+(schema
+ molecular-change.nonsense
+ (fields
+ [value
+ :enum
+ [:ochre-uaa-or-opal-uga
+ :amber-uag
+ :opal-uga
+ :ochre-uaa
+ :amber-uag-or-ochre-uaa
+ :amber-uag-or-opal-uga]]
+ [text :string]))
+
+(schema
+ molecular-change.splice-site
+ (fields [value :enum [:donor :acceptor]] [text :string]))
+
+(schema molecular-change.frameshift (fields [text :string]))
+
+(schema molecular-change.readthrough (fields [text :string]))
+
+(schema
+ structure-data
+ (fields
+ [id :string :unique-identity]
+ [evidence :ref :component]
+ [database :ref :many :component]
+ [protein :ref]
+ [selected :instant]
+ [cloned :instant]
+ [expressed :instant]
+ [soluble :instant]
+ [purified :instant]
+ [crystallized :instant]
+ [diffraction-quality-crystals :instant]
+ [diffraction :instant]
+ [native-diffraction-data :instant]
+ [phasing-diffraction-data :instant]
+ [nmr-assigned :instant]
+ [hsqc :instant]
+ [crystal-structure :instant]
+ [nmr-structure :instant]
+ [in-pdb :instant]
+ [in-bmrb :instant]
+ [work-stopped :instant]
+ [test-target :instant]
+ [other :instant]
+ [status-updated :instant]
+ [wormpep-release :long]
+ [remark :ref :many :component]))
+
+(schema
+ structure-data.database
+ (fields [database :ref] [field :ref] [accession :string :indexed]))
+
+(schema structure-data.remark (fields [text :string :indexed]))
+
+(schema
+ mass-spec-experiment
+ (fields
+ [id :string :unique-identity]
+ [reference :ref :many]
+ [remark :ref :many :component]
+ [laboratory :ref :many]
+ [person :ref :many]
+ [author :ref :many]
+ [species :ref]
+ [strain :ref]
+ [genotype :string :indexed :many]
+ [life-stage :ref :many]
+ [anatomy-term :ref :many]
+ [sub-cellular-localization :string :many]
+ [digestion :enum [:red-alk :trypsin]]
+ [ionisation-source :enum [:maldi :esi]]
+ [instrumentation :enum [:iontrap :qtof :ft]]
+ [database :string :many]
+ [program :string :many]
+ [minimum-ion-proportion :double]
+ [multiple-ambiguous-ids-allowed :boolean]
+ [minimum-peptide-length :long]
+ [false-discovery-rate :double]))
+
+(schema mass-spec-experiment.remark (fields [text :string]))
+
+(schema
+ mass-spec-peptide
+ (fields
+ [id :string :unique-identity]
+ [peptide :string]
+ [protein-seq :ref]
+ [petide-is-natural :boolean]
+ [mass-spec-experiments :ref :many :component]))
+
+(schema
+ mass-spec-peptide.mass-spec-experiments
+ (fields [mass-spec-experiment :ref]))
+
+(schema
+ mass-spec-data
+ (fields
+ [id :string :unique-identity]
+ [xcorr :double]
+ [deltacn :double]
+ [charge-state :long]
+ [sp-rank :long]
+ [sp-score :double]
+ [protein-probability :double]
+ [peptide-probability :double]
+ [matches-database-uniquely :boolean]
+ [protein :ref :many]))
+
+(schema
+ analysis
+ (fields
+ [id :string :unique-identity]
+ [database :ref :many :component]
+ [title :string :many]
+ [based-on-wb-release :long :many]
+ [based-on-db-release :string :many]
+ [project :ref :many]
+ [description :string :indexed :many]
+ [sample :ref :many]
+ [independent-variable
+ :enum
+ [:strain
+ :species
+ :life-stage
+ :sex
+ :exposure-time
+ :tissue
+ :food
+ :preparation
+ :treatment
+ :genotype
+ :temperature]
+ :many]
+ [species-in-analysis :ref :many]
+ [reference :ref :many]
+ [conducted-by :ref :many]
+ [url :string :many]))
+
+(schema
+ analysis.database
+ (fields [database :ref] [field :ref] [accession :string :indexed]))
+
+(schema
+ condition
+ (fields
+ [id :string :unique-identity]
+ [life-stage :ref :many]
+ [sex :enum [:hermaphrodite :female :unknown :male]]
+ [food :string :many]
+ [exposure-time :string :many]
+ [species :ref]
+ [strain :ref :many]
+ [preparation :string :indexed :many]
+ [temperature :double :many]
+ [genotype :string :indexed :many]
+ [other :string :indexed :many]
+ [contained-in :ref :many]
+ [follows :ref :many]
+ [reference :ref :many]
+ [tissue :ref :many]
+ [treatment :string :indexed :many]
+ [remark :ref :many :component]))
+
+(schema condition.remark (fields [text :string :indexed]))
+
+(schema
+ molecule
+ (fields
+ [id :string :unique-identity]
+ [public-name :string :indexed :many]
+ [formula :string :indexed :many]
+ [monoisotopic-mass :double :many]
+ [iupac :string :indexed :many]
+ [smiles :string :indexed :many]
+ [inchi :string :indexed :many]
+ [inchikey :string :indexed :many]
+ [synonym :string :indexed :many]
+ [database :ref :many :component]
+ [status :ref :many :component]
+ [detection-method :ref :many :component]
+ [extraction-method :ref :many :component]
+ [nonspecies-source :string :indexed :many]
+ [chemical-synthesis :ref :component]
+ [endogenous-in :ref :many :component]
+ [biofunction-role :ref :many :component]
+ [essential-for :ref :many :component]
+ [affects-phenotype-of-variation :ref :many :component]
+ [affects-phenotype-of-strain :ref :many :component]
+ [affects-phenotype-of-transgene :ref :many :component]
+ [affects-phenotype-of-rnai :ref :many :component]
+ [affects-phenotype-of-rearrangement :ref :many :component]
+ [use :ref :many :component]
+ [reference :ref :many]
+ [remark :ref :many :component]))
+
+(schema
+ molecule.database
+ (fields [database :ref] [database-field :ref] [text :string :indexed]))
+
+(schema molecule.status (fields [value :enum [:predicted :detected]]))
+
+(schema molecule.detection-method (fields [text :string :indexed]))
+
+(schema molecule.extraction-method (fields [text :string :indexed]))
+
+(schema molecule.endogenous-in (fields [species :ref]))
+
+(schema
+ molecule.biofunction-role
+ (fields
+ [value
+ :enum
+ [:structural-component
+ :product
+ :receptor
+ :cofactor
+ :inhibitor
+ :regulator
+ :activator
+ :metabolite
+ :ligand
+ :substrate]]
+ [text :string :indexed]))
+
+(schema molecule.essential-for (fields [species :ref]))
+
+(schema
+ molecule.affects-phenotype-of-variation
+ (fields [variation :ref] [phenotype :ref]))
+
+(schema
+ molecule.affects-phenotype-of-strain
+ (fields [strain :ref] [phenotype :ref]))
+
+(schema
+ molecule.affects-phenotype-of-transgene
+ (fields [transgene :ref] [phenotype :ref]))
+
+(schema
+ molecule.affects-phenotype-of-rnai
+ (fields [rnai :ref] [phenotype :ref]))
+
+(schema
+ molecule.affects-phenotype-of-rearrangement
+ (fields [rearrangement :ref] [phenotype :ref]))
+
+(schema molecule.use (fields [text :string :indexed]))
+
+(schema molecule.remark (fields [text :string :indexed]))
+
+(schema
+ wbprocess
+ (fields
+ [id :string :unique-identity]
+ [public-name :string :indexed]
+ [summary :ref :component]
+ [other-name :string :indexed :many]
+ [specialisation-of :ref :many]
+ [ncbi-taxonomy :string :indexed :many]
+ [gene :ref :many :component]
+ [expression-cluster :ref :many :component]
+ [interaction :ref :many :component]
+ [anatomy-term :ref :many :component]
+ [life-stage :ref :many :component]
+ [molecule :ref :many :component]
+ [gene-cluster :ref :many :component]
+ [phenotype :ref :many :component]
+ [go-term :ref :many :component]
+ [do-term :ref :many :component]
+ [marker-construct :ref :many]
+ [movie :ref :many :component]
+ [database :ref :many :component]
+ [remark :ref :many :component]
+ [historical-gene :ref :many :component]
+ [reference :ref :many]))
+
+(schema wbprocess.summary (fields [text :string :indexed]))
+
+(schema wbprocess.gene (fields [gene :ref]))
+
+(schema wbprocess.expression-cluster (fields [expression-cluster :ref]))
+
+(schema wbprocess.interaction (fields [interaction :ref]))
+
+(schema wbprocess.anatomy-term (fields [anatomy-term :ref]))
+
+(schema wbprocess.life-stage (fields [life-stage :ref]))
+
+(schema wbprocess.molecule (fields [molecule :ref]))
+
+(schema wbprocess.gene-cluster (fields [gene-cluster :ref]))
+
+(schema wbprocess.phenotype (fields [phenotype :ref]))
+
+(schema wbprocess.go-term (fields [go-term :ref]))
+
+(schema wbprocess.do-term (fields [do-term :ref]))
+
+(schema wbprocess.movie (fields [movie :ref]))
+
+(schema
+ wbprocess.database
+ (fields [database :ref] [field :ref] [accession :string :indexed]))
+
+(schema wbprocess.remark (fields [text :string :indexed]))
+
+(schema wbprocess.historical-gene (fields [gene :ref] [text :string]))
+
+(schema homol-data (fields [id :string :unique-identity]))
+
+(schema feature-data (fields [id :string :unique-identity]))
+
+(schema
+ keyword
+ (fields [id :string :unique-identity "Built-in ?Keyword type."]))
+
diff --git a/project.clj b/project.clj
index 0cb508f..7510da5 100755
--- a/project.clj
+++ b/project.clj
@@ -1,4 +1,4 @@
-(defproject wormbase/pseudoace "0.4.10"
+(defproject wormbase/pseudoace "0.4.11"
:dependencies [[clj-time "0.12.0"]
[datomic-schema "1.3.0"]
[org.clojure/clojure "1.8.0"]
@@ -23,23 +23,33 @@
:main pseudoace.core
:target-path "target/%s"
:profiles {:uberjar {:aot :all}
- :test {:resource-paths ["test/resources"]}
- :dev {:dependencies [[datomic-schema-grapher "0.0.1"]]
- :plugins [[jonase/eastwood "0.2.3"]
- [lein-ancient "0.6.8"]
- [lein-bikeshed "0.3.0"]
- [lein-kibit "0.1.2"]
- [lein-ns-dep-graph "0.1.0-SNAPSHOT"]]
- :resource-paths ["test/resources"]}
- :datomic-free {:dependencies [[com.datomic/datomic-free "0.9.5385"
- :exclusions [joda-time]]]
- :exclusions [com.datomic/datomic-pro]}
- :datomic-pro {:dependencies [[com.datomic/datomic-pro "0.9.5385"
- :exclusions [joda-time]]]}
- :mysql {:dependencies [[mysql/mysql-connector-java "6.0.2"]]}
- :postgresql {:dependencies [[org.postgresql/postgresql "9.4.1209"]]}
- :ddb {:dependencies [[com.amazonaws/aws-java-sdk-dynamodb "1.11.6"
- :exclusions [joda-time]]]}}
+ :datomic-free [{:dependencies
+ [[com.datomic/datomic-free "0.9.5385"
+ :exclusions [joda-time]]]}]
+ :datomic-pro [{:dependencies
+ [[com.datomic/datomic-pro "0.9.5385"
+ :exclusions [joda-time]]]}]
+ :test [{:resource-paths ["test/resources"]}]
+ :ddb [:datomic-pro
+ {:dependencies
+ [[com.amazonaws/aws-java-sdk-dynamodb "1.11.6"
+ :exclusions [joda-time]]]}]
+ :dev [{:dependencies [[datomic-schema-grapher "0.0.1"]]
+ :plugins [[jonase/eastwood "0.2.3"]
+ [lein-ancient "0.6.8"]
+ [lein-bikeshed "0.3.0"]
+ [lein-kibit "0.1.2"]
+ [lein-ns-dep-graph "0.1.0-SNAPSHOT"]]
+ :resource-paths ["test/resources"]}]
+ :dev-ddb [:ddb :dev]
+ :dev-free [:datomic-free :dev]
+ :dev-mysql [:dev
+ {:dependencies
+ [[mysql/mysql-connector-java "6.0.2"]]}]
+ :dev-postgresql [:dev
+ {:dependencies
+ [[org.postgresql/postgresql "9.4.1209"]]}]
+ :prod [:ddb]}
:deploy-repositories [["releases" :clojars]]
:repositories {"my.datomic.com" {:url "https://my.datomic.com/repo"
:creds :gpg}})
diff --git a/src/pseudoace/core.clj b/src/pseudoace/core.clj
index 300e9ce..38b6ff5 100644
--- a/src/pseudoace/core.clj
+++ b/src/pseudoace/core.clj
@@ -274,8 +274,10 @@
(defn import-logs
"Import the sorted EDN log files."
- [& {:keys [url log-dir verbose]
- :or {verbose false}}]
+ [& {:keys [url log-dir partition-max-count partition-max-text verbose]
+ :or {verbose false
+ partition-max-count 1000
+ partition-max-text 5000}}]
(if verbose
(println "Importing logs into datomic" url log-dir verbose))
(let [con (d/connect url)
@@ -289,7 +291,9 @@
(println \tab "importing: " (.getName file)))
(ts-import/play-logfile
con
- (java.util.zip.GZIPInputStream. (io/input-stream file))))
+ (java.util.zip.GZIPInputStream. (io/input-stream file))
+ partition-max-count
+ partition-max-text))
(d/release con)))
(defn excise-tmp-data
@@ -315,7 +319,9 @@
results (d/q datalog-query (d/db con))
n-results (count results)]
(when verbose
- (println "Testing datomic data, expecting exactly" n-expected "result")
+ (println "Testing datomic data, expecting exactly"
+ n-expected
+ "result")
(println "Datalog query:" datalog-query)
(print "Results: ")
(pprint results))
@@ -326,8 +332,11 @@
(defn import-helper-edn-logs
"Import the helper log files."
- [& {:keys [url log-dir verbose]
- :or {verbose false}}]
+ [& {:keys
+ [url log-dir partition-max-count partition-max-text verbose]
+ :or {partition-max-count 1000
+ partition-max-text 5000
+ verbose false}}]
(if verbose
(println "Importing helper log into helper database"))
(let [helper-uri (uri-to-helper-uri url)
@@ -336,7 +345,9 @@
(ts-import/play-logfile
helper-connection
(java.util.zip.GZIPInputStream.
- (io/input-stream (helper-dest-file log-dir)))))
+ (io/input-stream (helper-dest-file log-dir)))
+ partition-max-count
+ partition-max-text))
(if verbose
(println \tab "Releasing helper database connection"))
(d/release helper-connection)))
@@ -358,7 +369,8 @@
(run-locatables-importer-for-helper url acedump-dir :verbose false))
([url log-dir acedump-dir verbose]
(if verbose
- (println "Importing logs with loactables importer into helper database"))
+ (println (str "Importing logs with loactables "
+ "importer into helper database")))
(let [helper-uri (uri-to-helper-uri url)
helper-connection (d/connect helper-uri)
helper-db (d/db helper-connection)
@@ -436,9 +448,10 @@
(let [write-line (fn [line]
(.write writer line)
(.newLine writer))
- header-line (tab-join (map
- format-left
- ["Class" "Missing" "Added" "Identical"]))]
+ header-line
+ (tab-join (map
+ format-left
+ ["Class" "Missing" "Added" "Identical"]))]
(write-line header-line)
(if verbose
(println header-line))
@@ -451,7 +464,9 @@
counts [n-ref-only n-db-only n-both]
f-counts (map format-num counts)
out-line (tab-join
- (map format-left (concat [class-name] f-counts)))]
+ (map
+ format-left
+ (concat [class-name] f-counts)))]
(write-line out-line)
(if verbose
(println out-line))
@@ -460,7 +475,8 @@
qa/write-class-ids
class-ids-dir
class-name)
- label-suffix (if (and (= n-ref-only n-db-only)
+ label-suffix (if
+ (and (= n-ref-only n-db-only)
(not= n-ref-only n-db-only 0))
"_bad-identifiers"
"")]
@@ -545,7 +561,11 @@
action-docs (vals cli-doc-map)
doc-width-left (+ 10 (apply max (map count action-docs)))
action-width-right (+ 10 (apply max (map count action-names)))
- line-template (str "%-" action-width-right "s%-" doc-width-left "s")]
+ line-template (str "%-"
+ action-width-right
+ "s%-"
+ doc-width-left
+ "s")]
(str/join
\newline
(concat
diff --git a/src/pseudoace/ts_import.clj b/src/pseudoace/ts_import.clj
index 6ce0b6e..2828bf8 100755
--- a/src/pseudoace/ts_import.clj
+++ b/src/pseudoace/ts_import.clj
@@ -861,27 +861,28 @@
ffirst
from-date)))
-(defn play-logfile [con logfile]
- (with-open [r (reader logfile)]
- (doseq [rblk (partition-log 100 5000 (logfile-seq r))] ;; was 1000 50000
- (doseq [sblk (partition-by first rblk)
- :let [stamp (ffirst sblk)]]
- (let [blk (map second sblk)
- db (d/db con)
- fdatoms (filter (fn [[_ _ _ v]] (not (map? v))) blk)
- tx-meta (txmeta stamp)
- datoms (fixup-datoms db fdatoms)
- ms->s #(/ 1000 %)
- imp-tx-secs (ms->s (-> tx-meta
- :db/txInstant
- (.getTime)))
- last-db-tx-secs (ms->s (-> db
- latest-transaction-date
- to-date
- (.getTime)))]
- (if (<= imp-tx-secs last-db-tx-secs)
- (try
- @(d/transact-async con (conj datoms tx-meta))
- (catch Throwable t
- (.printStackTrace t)))
- (println "Skipping transaction with past-date:" stamp)))))))
+(defn play-logfile
+ [con logfile max-count max-text]
+ (with-open [r (reader logfile)]
+ (doseq [rblk (partition-log max-count max-text (logfile-seq r))]
+ (doseq [sblk (partition-by first rblk)
+ :let [stamp (ffirst sblk)]]
+ (let [blk (map second sblk)
+ db (d/db con)
+ fdatoms (filter (fn [[_ _ _ v]] (not (map? v))) blk)
+ tx-meta (txmeta stamp)
+ datoms (fixup-datoms db fdatoms)
+ ms->s #(/ 1000 %)
+ imp-tx-secs (ms->s (-> tx-meta
+ :db/txInstant
+ (.getTime)))
+ last-db-tx-secs (ms->s (-> db
+ latest-transaction-date
+ to-date
+ (.getTime)))]
+ (if (<= imp-tx-secs last-db-tx-secs)
+ (try
+ @(d/transact-async con (conj datoms tx-meta))
+ (catch Throwable t
+ (.printStackTrace t)))
+ (println "Skipping transaction with past-date:" stamp)))))))