Constant Field Values

Contents

• psidev.psi.*

psidev.psi.*

psidev.psi.mi.jami.binary.expansion.ComplexExpansionMethod<T extends Interaction,B extends BinaryInteraction>

Modifier and Type	Constant Field	Value
public static final String	BIPARTITE	"bipartite"
public static final String	BIPARTITE_EXPANSION	"bipartite expansion"
public static final String	BIPARTITE_EXPANSION_MI	"MI:1062"
public static final String	MATRIX	"matrix expansion"
public static final String	MATRIX_EXPANSION	"matrix expansion"
public static final String	MATRIX_EXPANSION_MI	"MI:1061"
public static final String	SPOKE	"spoke"
public static final String	SPOKE_EXPANSION	"spoke expansion"
public static final String	SPOKE_EXPANSION_MI	"MI:1060"

psidev.psi.mi.jami.bridges.chebi.CachedChebiFetcher

Modifier and Type	Constant Field	Value
public static final String	CHEBI_CACHE_NAME	"chebi-cache"

psidev.psi.mi.jami.bridges.chebi.ChebiFetcher

Modifier and Type	Constant Field	Value
public static final String	CHEBI_POLYSACCHARYDE_PARENT	"CHEBI:18154"

psidev.psi.mi.jami.bridges.europubmedcentral.CachedEuroPubmedCentralFetcher

Modifier and Type	Constant Field	Value
public static final String	CACHE_NAME	"europubmedcentral-service-cache"

psidev.psi.mi.jami.bridges.fetcher.AbstractCachedFetcher

Modifier and Type	Constant Field	Value
public static final String	EHCACHE_CONFIG_FILE	"/service.ehcache.xml"

psidev.psi.mi.jami.bridges.imex.Constants

Modifier and Type	Constant Field	Value
public static final String	IMEX_DB_CURATORS_SUFFIX	" CURATORS"
public static final String	IMEX_NAME	"IMEX"
public static final String	INTACT_ADMIN	"INTACT"

psidev.psi.mi.jami.bridges.imex.ImexCentralClient

Modifier and Type	Constant Field	Value
public static final String	IC_BETA	"https://imexcentral.org/icentralbeta/ws-v20"
public static final String	IC_PROD	"https://imexcentral.org/icentral/ws-v20"
public static final String	IC_TEST	"https://imexcentral.org/icentraltest/ws-v20"
public static final int	IDENTIFIER_MISSING	4
public static final int	IDENTIFIER_UNKNOWN	5
public static final int	INTERNAL_SERVER_ERROR	99
public static final int	NO_IMEX_ID	9
public static final int	NO_RECORD	6
public static final int	NO_RECORD_CREATED	7
public static final int	OPERATION_NOT_SUPPORTED	98
public static final int	OPERATION_NOT_VALID	3
public static final int	STATUS_UNKNOWN	8
public static final int	UNKNOWN_GROUP	11
public static final int	UNKNOWN_USER	10
public static final int	USER_NOT_AUTHORIZED	2

psidev.psi.mi.jami.bridges.mapper.listener.ProteinMappingStatisticsWriter

Modifier and Type	Constant Field	Value
public static final String	NEW_EVENT	"\t"
public static final String	NEW_LINE	"\n"

psidev.psi.mi.jami.bridges.obo.AbstractOboLoader<T extends CvTerm>

Modifier and Type	Constant Field	Value
public static final String	ALIAS_IDENTIFIER	"Alternate label curated by PSI-MI"
public static final String	COMMENT_KEY	"comment"
public static final String	EXACT_KEY	"exact"
public static final String	GO	"go"
public static final String	GO_MI_REF	"MI:0448"
public static final String	HTTP_DEF	"http"
public static final String	LINE_BREAK	"\n"
public static final String	META_XREF_SEPARATOR	":"
public static final String	METHOD_REFERENCE	"method reference"
public static final String	METHOD_REFERENCE_MI_REF	"MI:0357"
public static final String	MOD_ALIAS_IDENTIFIER	"Alternate name curated by PSI-MOD"
public static final String	MOD_SHORTLABEL_IDENTIFIER	"Short label curated by PSI-MOD"
public static final String	PMID	"PMID"
public static final String	PMID_APPLICATION	"PMID for application instance"
public static final String	QUOTE	"""
public static final String	RESID	"resid"
public static final String	RESID_IDENTIFIER	"Alternate name from RESID"
public static final String	RESID_MI_REF	"MI:0248"
public static final String	RESID_MISNOMER_IDENTIFIER	"Misnomer tagged alternate name from RESID"
public static final String	RESID_NAME_IDENTIFIER	"Name from RESID"
public static final String	RESID_SYSTEMATIC_IDENTIFIER	"Systematic name from RESID"
public static final String	SEARCH_URL	"search-url"
public static final String	SEARCH_URL_MI_REF	"MI:0615"
public static final String	SHORTLABEL_IDENTIFIER	"Unique short label curated by PSI-MI"
public static final String	SO	"so"
public static final String	SO_MI_REF	"MI:0601"
public static final String	UNIPROT_FEATURE_IDENTIFIER	"Protein feature description from UniProtKB"
public static final int	XREF_TYPE	3
public static final String	XREF_VALIDATION_REGEXP	"id-validation-regexp"
public static final String	XREF_VALIDATION_REGEXP_MI_REF	"MI:0628"

psidev.psi.mi.jami.bridges.obo.OntologyOboLoader

Modifier and Type	Constant Field	Value
protected static final String	COMMENT_KEY	"comment"
protected static final String	EXACT_KEY	"exact"
protected static final String	LINE_BREAK	"\n"
protected static final String	META_XREF_SEPARATOR	":"
protected static final String	METHOD_REFERENCE	"method reference"
protected static final String	METHOD_REFERENCE_MI_REF	"MI:0357"
protected static final String	PMID	"PMID"
protected static final String	RESID	"resid"
protected static final String	RESID_MI_REF	"MI:0248"
protected static final int	XREF_TYPE	3

psidev.psi.mi.jami.bridges.ols.CachedOlsCvTermFetcher

Modifier and Type	Constant Field	Value
public static final String	CACHE_NAME	"cvterm-cache"

psidev.psi.mi.jami.bridges.ols.CachedOlsOntologyTermFetcher

Modifier and Type	Constant Field	Value
public static final String	CACHE_NAME	"ontology-cache"

psidev.psi.mi.jami.bridges.ols.CachedOlsSourceFetcher

Modifier and Type	Constant Field	Value
public static final String	CACHE_NAME	"source-cache"

psidev.psi.mi.jami.bridges.ols.utils.OlsUtils

Modifier and Type	Constant Field	Value
public static final String	COMMENT_KEY	"comment"
public static final String	DEFINITION_KEY	"definition"
public static final String	EXACT_SYNONYM_KEY	"exact_synonym"
public static final String	HTTP_DEF	"http"
public static final String	META_DATA_SEPARATOR	"_"
public static final String	META_XREF_SEPARATOR	":"
public static final String	MI_ALIAS_IDENTIFIER	"Alternate label curated by PSI-MI"
public static final String	MI_SHORTLABEL_IDENTIFIER	"Unique short label curated by PSI-MI"
public static final String	MOD_ALIAS_IDENTIFIER	"Alternate name curated by PSI-MOD"
public static final String	MOD_SHORTLABEL_IDENTIFIER	"Short label curated by PSI-MOD"
public static final String	PMID	"PMID"
public static final String	PMID_APPLICATION	"PMID for application instance"
public static final String	QUOTE	"""
public static final String	RESID_IDENTIFIER	"Alternate name from RESID"
public static final String	RESID_MISNOMER_IDENTIFIER	"Misnomer tagged alternate name from RESID"
public static final String	RESID_NAME_IDENTIFIER	"Name from RESID"
public static final String	RESID_SYSTEMATIC_IDENTIFIER	"Systematic name from RESID"
public static final String	UNIPROT_FEATURE_IDENTIFIER	"Protein feature description from UniProtKB"
public static final String	XREF_DEFINITION_KEY	"xref_definition"

psidev.psi.mi.jami.bridges.uniprot.CachedUniprotGeneFetcher

Modifier and Type	Constant Field	Value
public static final String	CACHE_NAME	"uniprot-gene-service-cache"
public static final String	EHCACHE_CONFIG_FILE	"/service.ehcache.xml"

psidev.psi.mi.jami.bridges.uniprot.CachedUniprotProteinFetcher

Modifier and Type	Constant Field	Value
public static final String	CACHE_NAME	"uniprot-service-cache"

psidev.psi.mi.jami.bridges.uniprot.taxonomy.CachedUniprotTaxonomyFetcher

Modifier and Type	Constant Field	Value
public static final String	CACHE_NAME	"uniprot-taxonomy-service-cache"

psidev.psi.mi.jami.bridges.uniprot.util.UniprotUtils

Modifier and Type	Constant Field	Value
public static final String	FEATURE_CHAIN_FIELD	"feature.chain:"
public static final String	FEATURE_PEPTIDE_FIELD	"feature.peptide:"
public static final String	FEATURE_PRO_PEPTIDE_FIELD	"feature.propep:"

psidev.psi.mi.jami.bridges.unisave.CachedUnisaveClient

Modifier and Type	Constant Field	Value
public static final String	CACHE_NAME	"unisave-service-cache"

psidev.psi.mi.jami.commons.MIFileAnalyzer

Modifier and Type	Constant Field	Value
public static final String	MITAB_25_TITLE	"#ID(s) interactor A\tID(s) interactor B\tAlt. ID(s) interactor A\tAlt. ID(s) interactor B\tAlias(es) interactor A\tAlias(es) interactor B\tInteraction detection method(s)\tPublication 1st author(s)\tPublication Identifier(s)\tTaxid interactor A\tTaxid interactor B\tInteraction type(s)\tSource database(s)\tInteraction identifier(s)\tConfidence value(s)"

psidev.psi.mi.jami.crosslink.CsvDatasourceOptions

Modifier and Type	Constant Field	Value
public static final String	CROSSLINK_CSV_FORMAT	"crosslink_csv"
public static final String	CSV_TYPE_OPTION_KEY	"crosslink_csv_type_key"

psidev.psi.mi.jami.crosslink.utils.CsvUtils

Modifier and Type	Constant Field	Value
public static final String	CROSS_LINK	"crosslink"
public static final String	CROSS_LINK_MI	"MI:0030"
public static final String	CROSS_LINKER	"cross linker"
public static final String	CROSS_LINKER_MI	"MI:0911"
public static final String	PHYSICAL_INTERACTION	"physical association"
public static final String	PHYSICAL_INTERACTION_MI	"MI:0915"
public static final String	PROTEIN_SEPARATOR	";"
public static final String	SEQUENCE_TAG	"sequence tag"
public static final String	SEQUENCE_TAG_MI	"MI:0102"
public static final String	XREF_SEPARATOR	"|"

psidev.psi.mi.jami.datasource.MIFileDataSource

Modifier and Type	Constant Field	Value
public static final String	FILE_URI_PREFIX	"file://"

psidev.psi.mi.jami.enricher.impl.minimal.MinimalProteinEnricher

Modifier and Type	Constant Field	Value
public static final String	CAUTION_MESSAGE	"This sequence has been withdrawn from Uniprot."

psidev.psi.mi.jami.enricher.impl.minimal.MinimalProteinUpdater

Modifier and Type	Constant Field	Value
public static final String	UNIPROT_REMOVED_QUALIFIER	"uniprot-removed-ac"

psidev.psi.mi.jami.enricher.listener.impl.writer.BioactiveEntityEnricherStatisticsWriter

Modifier and Type	Constant Field	Value
public static final String	FILE_NAME	"bioactive_entity"

psidev.psi.mi.jami.enricher.listener.impl.writer.EnricherStatisticsWriter<T>

Modifier and Type	Constant Field	Value
public static final String	FAILURE_SUFFIX	"_failed.csv"
public static final String	SUCCESS_SUFFIX	"_success.csv"

psidev.psi.mi.jami.enricher.listener.impl.writer.GeneEnricherStatisticsWriter

Modifier and Type	Constant Field	Value
public static final String	FILE_NAME	"Gene"

psidev.psi.mi.jami.enricher.listener.impl.writer.InteractorEnricherStatisticsWriter<T extends Interactor>

Modifier and Type	Constant Field	Value
public static final String	FILE_NAME	"interactor"

psidev.psi.mi.jami.enricher.util.EnricherUtils

Modifier and Type	Constant Field	Value
public static final String	BLANK_SPACE	"-"
public static final String	COLUMN_SEPARATOR	"\t"
public static final String	NEW_LINE	"\n"

psidev.psi.mi.jami.factory.options.InteractionWriterOptions

Modifier and Type	Constant Field	Value
public static final String	COMPLEX_EXPANSION_OPTION_KEY	"complex_expansion_key"
public static final String	COMPLEX_TYPE_OPTION_KEY	"complex_type_key"
public static final String	INTERACTION_CATEGORY_OPTION_KEY	"interaction_category_key"
public static final String	OUTPUT_FORMAT_OPTION_KEY	"output_format_key"
public static final String	OUTPUT_OPTION_KEY	"output_key"

psidev.psi.mi.jami.factory.options.MIDataSourceOptions

Modifier and Type	Constant Field	Value
public static final String	COMPLEX_EXPANSION_OPTION_KEY	"complex_expansion_key"
public static final String	COMPLEX_TYPE_OPTION_KEY	"complex_type_key"
public static final String	INPUT_TYPE_OPTION_KEY	"input_format_key"
public static final String	INTERACTION_CATEGORY_OPTION_KEY	"interaction_category_key"
public static final String	INTERACTOR_FACTORY_OPTION_KEY	"interactor_factory_key"
public static final String	STREAMING_OPTION_KEY	"streaming_key"

psidev.psi.mi.jami.factory.options.MIFileDataSourceOptions

Modifier and Type	Constant Field	Value
public static final String	INPUT_OPTION_KEY	"input_key"
public static final String	PARSER_LISTENER_OPTION_KEY	"parser_listener_key"

psidev.psi.mi.jami.html.utils.HtmlWriterOptions

Modifier and Type	Constant Field	Value
public static final String	MI_HTML_FORMAT	"mi_html"
public static final String	WRITE_HTML_HEADER_BODY_OPTION	"write_html_header_option_key"

psidev.psi.mi.jami.imex.actions.PublicationIdentifierSynchronizer

Modifier and Type	Constant Field	Value
public static final String	INTERNAL	"jint"

psidev.psi.mi.jami.json.MIJsonUtils

Modifier and Type	Constant Field	Value
public static final String	CLOSE	"}"
public static final String	CLOSE_ARRAY	"]"
public static final String	ELEMENT_SEPARATOR	","
public static final String	INDENT	"\t"
public static final String	OPEN	"{"
public static final String	OPEN_ARRAY	"["
public static final String	PROPERTY_DELIMITER	"\""
public static final String	PROPERTY_VALUE_SEPARATOR	":"

psidev.psi.mi.jami.json.MIJsonWriterOptions

Modifier and Type	Constant Field	Value
public static final String	MI_JSON_FORMAT	"interaction_viewer_json"
public static final String	MI_JSON_TYPE	"interaction_viewer_json_type"
public static final String	ONTOLOGY_FETCHER_OPTION_KEY	"ontology_fetcher_key"

psidev.psi.mi.jami.model.Alias

Modifier and Type	Constant Field	Value
public static final String	AUTHOR_ASSIGNED_NAME	"author assigned name"
public static final String	AUTHOR_ASSIGNED_NAME_MI	"MI:0345"
public static final String	COMPLEX_RECOMMENDED_NAME	"complex recommended name"
public static final String	COMPLEX_RECOMMENDED_NAME_MI	"MI:1315"
public static final String	COMPLEX_SYNONYM	"complex-synonym"
public static final String	COMPLEX_SYNONYM_MI	"MI:0673"
public static final String	COMPLEX_SYSTEMATIC_NAME	"complex systematic name"
public static final String	COMPLEX_SYSTEMATIC_NAME_MI	"MI:1316"
public static final String	GENE_NAME	"gene name"
public static final String	GENE_NAME_MI	"MI:0301"
public static final String	GENE_NAME_SYNONYM	"gene name synonym"
public static final String	GENE_NAME_SYNONYM_MI	"MI:0302"
public static final String	ISOFORM_SYNONYM	"gene name synonym"
public static final String	ISOFORM_SYNONYM_MI	"MI:0304"
public static final String	IUPAC	"iupac name"
public static final String	IUPAC_MI	"MI:2007"
public static final String	LOCUS_NAME	"locus name"
public static final String	LOCUS_NAME_MI	"MI:0305"
public static final String	ORF_NAME	"orf name"
public static final String	ORF_NAME_MI	"MI:0306"
public static final String	SYNONYM	"synonym"
public static final String	SYNONYM_MI	"MI:1041"

psidev.psi.mi.jami.model.Annotation

Modifier and Type	Constant Field	Value
public static final String	AUTHOR	"author-list"
public static final String	AUTHOR_MI	"MI:0636"
public static final String	BIPARTITE_EXPANSION	"bipartite expansion"
public static final String	BIPARTITE_EXPANSION_MI	"MI:1062"
public static final String	CAUTION	"caution"
public static final String	CAUTION_MI	"MI:0618"
public static final String	CLUSTERED	"clustered"
public static final String	CLUSTERED_MI	"MI:1052"
public static final String	COMMENT	"comment"
public static final String	COMMENT_MI	"MI:0612"
public static final String	COMPLEX_EXPANSION	"complex expansion"
public static final String	COMPLEX_EXPANSION_MI	"MI:1059"
public static final String	COMPLEX_PROPERTIES	"complex-properties"
public static final String	COMPLEX_PROPERTIES_MI	"MI:0629"
public static final String	CONTACT_EMAIL	"contact-email"
public static final String	CONTACT_EMAIL_MI	"MI:0634"
public static final String	CURATION_DEPTH	"curation depth"
public static final String	CURATION_DEPTH_MI	"MI:0955"
public static final String	EVIDENCE	"evidence"
public static final String	EVIDENCE_MI	"MI:1051"
public static final String	EXP_MODIFICATION	"experiment modification"
public static final String	EXP_MODIFICATION_MI	"MI:0627"
public static final String	EXPERIMENTALLY_OBSERVED	"experimentally-observed"
public static final String	EXPERIMENTALLY_OBSERVED_MI	"MI:1054"
public static final String	FIGURE_LEGEND	"figure legend"
public static final String	FIGURE_LEGEND_MI	"MI:0599"
public static final String	FULL_COVERAGE	"full coverage"
public static final String	FULL_COVERAGE_MI	"MI:0957"
public static final String	IMEX_CURATION	"imex curation"
public static final String	IMEX_CURATION_MI	"MI:0959"
public static final String	IMPORTED	"imported"
public static final String	IMPORTED_MI	"MI:1058"
public static final String	INTERNALLY_CURATED	"internally-curated"
public static final String	INTERNALLY_CURATED_MI	"MI:1055"
public static final String	MATRIX_EXPANSION	"matrix expansion"
public static final String	MATRIX_EXPANSION_MI	"MI:1061"
public static final String	MIMIX_CURATION	"mimix curation"
public static final String	MIMIX_CURATION_MI	"MI:0960"
public static final String	NUCLEIC_ACID_PROTEIN	"nucleicacid-protein"
public static final String	NUCLEIC_ACID_PROTEIN_MI	"MI:1049"
public static final String	PARTIAL_COVERAGE	"partial coverage"
public static final String	PARTIAL_COVERAGE_MI	"MI:0958"
public static final String	POSTAL_ADDRESS	"postaladdress"
public static final String	PREDICTED	"predicted"
public static final String	PREDICTED_MI	"MI:1057"
public static final String	PROTEIN_PROTEIN	"protein-protein"
public static final String	PROTEIN_PROTEIN_MI	"MI:1047"
public static final String	PUBLICATION_JOURNAL	"journal"
public static final String	PUBLICATION_JOURNAL_MI	"MI:0885"
public static final String	PUBLICATION_TITLE	"publication title"
public static final String	PUBLICATION_TITLE_MI	"MI:1091"
public static final String	PUBLICATION_YEAR	"publication year"
public static final String	PUBLICATION_YEAR_MI	"MI:0886"
public static final String	RAPID_CURATION	"rapid curation"
public static final String	RAPID_CURATION_MI	"MI:0961"
public static final String	SEARCH_URL	"search-url"
public static final String	SEARCH_URL_MI	"MI:0615"
public static final String	SMALL_MOLECULE_PROTEIN	"smallmolecule-protein"
public static final String	SMALL_MOLECULE_PROTEIN_MI	"MI:1048"
public static final String	SPOKE_EXPANSION	"spoke expansion"
public static final String	SPOKE_EXPANSION_MI	"MI:1060"
public static final String	TEXT_MINING	"text-mining"
public static final String	TEXT_MINING_MI	"MI:1056"
public static final String	URL	"url"
public static final String	URL_MI	"MI:0614"
public static final String	VALIDATION_REGEXP	"id-validation-regexp"
public static final String	VALIDATION_REGEXP_MI	"MI:0628"

psidev.psi.mi.jami.model.BioactiveEntity

Modifier and Type	Constant Field	Value
public static final String	BIOACTIVE_ENTITY	"bioactive entity"
public static final String	BIOACTIVE_ENTITY_MI	"MI:1100"
public static final String	POLYSACCHARIDE	"polysaccharide"
public static final String	POLYSACCHARIDE_MI	"MI:0904"
public static final String	SMALL_MOLECULE	"small molecule"
public static final String	SMALL_MOLECULE_MI	"MI:0328"

psidev.psi.mi.jami.model.Checksum

Modifier and Type	Constant Field	Value
public static final String	CHECKSUM_MI	"MI:1212"
public static final String	CHECKUM	"checksum"
public static final String	INCHI	"stamdard inchi"
public static final String	INCHI_KEY	"inchi key"
public static final String	INCHI_KEY_MI	"MI:0970"
public static final String	INCHI_MI	"MI:2010"
public static final String	INCHI_SHORT	"inchi id"
public static final String	IRIGID	"irigid"
public static final String	IROGID	"irogid"
public static final String	RIGID	"rigid"
public static final String	RIGID_MI	"MI:1334"
public static final String	ROGID	"rogid"
public static final String	ROGID_MI	"MI:1333"
public static final String	SMILE	"smiles string"
public static final String	SMILE_MI	"MI:2039"
public static final String	SMILE_SHORT	"smile"
public static final String	STANDARD_INCHI_KEY	"standard inchi key"
public static final String	STANDARD_INCHI_KEY_MI	"MI:1101"

psidev.psi.mi.jami.model.Complex

Modifier and Type	Constant Field	Value
public static final String	COMPLEX	"complex"
public static final String	COMPLEX_MI	"MI:0314"

psidev.psi.mi.jami.model.Confidence

Modifier and Type	Constant Field	Value
public static final String	AUTHOR_BASED_CONFIDENCE	"author-based confidence"
public static final String	AUTHOR_BASED_CONFIDENCE_MI	"MI:1221"

psidev.psi.mi.jami.model.CooperativeEffect

Modifier and Type	Constant Field	Value
public static final String	AFFECTED_INTERACTION	"affected interaction"
public static final String	AFFECTED_INTERACTION_ID	"MI:1150"
public static final String	ALLOSTERIC_DYNAMIC_CHANGE	"allosteric change in dynamics"
public static final String	ALLOSTERIC_DYNAMIC_CHANGE_ID	"MI:1166"
public static final String	ALLOSTERIC_EFFECTOR	"allosteric effector"
public static final String	ALLOSTERIC_EFFECTOR_ID	"MI:1160"
public static final String	ALLOSTERIC_K_RESPONSE	"allosteric k-type response"
public static final String	ALLOSTERIC_K_RESPONSE_ID	"MI:1162"
public static final String	ALLOSTERIC_MOLECULE	"allosteric molecule"
public static final String	ALLOSTERIC_MOLECULE_ID	"MI:1159"
public static final String	ALLOSTERIC_PTM	"allosteric ptm"
public static final String	ALLOSTERIC_PTM_ID	"MI:1175"
public static final String	ALLOSTERIC_STRUCTURE_CHANE	"allosteric change in structure"
public static final String	ALLOSTERIC_STRUCTURE_CHANE_ID	"MI:1165"
public static final String	ALLOSTERIC_V_RESPONSE	"allosteric v-type response"
public static final String	ALLOSTERIC_V_RESPONSE_ID	"MI:1163"
public static final String	ALLOSTERY	"allostery"
public static final String	ALLOSTERY_ID	"MI:1157"
public static final String	ALTERED_PHYSICO_COMPATIBILITY	"altered physicochemical compatibility"
public static final String	ALTERED_PHYSICO_COMPATIBILITY_ID	"MI:1172"
public static final String	BINDING_HIDING	"binding site hiding"
public static final String	BINDING_HIDING_ID	"MI:1173"
public static final String	COMPOSITE_BINDING	"composite binding site formation"
public static final String	COMPOSITE_BINDING_ID	"MI:1171"
public static final String	COOPERATIVE_EFFECT_VALUE	"cooperative effect value"
public static final String	COOPERATIVE_EFFECT_VALUE_ID	"MI:1152"
public static final String	EFFECT_OUTCOME	"cooperative effect outcome"
public static final String	EFFECT_OUTCOME_MI	"MI:1153"
public static final String	HETEROTROPIC_ALLOSTERY	"heterotropic allostery"
public static final String	HETEROTROPIC_ALLOSTERY_ID	"MI:1168"
public static final String	HOMOTROPIC_ALLOSTERY	"homotropic allostery"
public static final String	HOMOTROPIC_ALLOSTERY_ID	"MI:1169"
public static final String	NEGATIVE_EFFECT	"negative cooperative effect"
public static final String	NEGATIVE_EFFECT_ID	"MI:1155"
public static final String	PARTICIPANT_REF	"participant-ref"
public static final String	PARTICIPANT_REF_ID	"MI:1151"
public static final String	POSITIVE_EFFECT	"positive cooperative effect"
public static final String	POSITIVE_EFFECT_ID	"MI:1154"
public static final String	PRE_ORGANIZATION	"configurational pre-organization"
public static final String	PRE_ORGANIZATION_ID	"MI:1174"
public static final String	PREASSEMBLY	"pre-assembly"
public static final String	PREASSEMBLY_ID	"MI:1158"

psidev.psi.mi.jami.model.CvTerm

Modifier and Type	Constant Field	Value
public static final String	PSI_MI	"psi-mi"
public static final String	PSI_MI_MI	"MI:0488"
public static final String	PSI_MOD	"psi-mod"
public static final String	PSI_MOD_MI	"MI:0897"
public static final String	PSI_PAR	"psi-par"

psidev.psi.mi.jami.model.Experiment

Modifier and Type	Constant Field	Value
public static final String	INFERRED_BY_CURATOR	"inferred by curator"
public static final String	INFERRED_BY_CURATOR_MI	"MI:0364"
public static final String	UNSPECIFIED_METHOD	"unspecified method"
public static final String	UNSPECIFIED_METHOD_MI	"MI:0686"

psidev.psi.mi.jami.model.Feature<P extends Entity,F extends Feature>

Modifier and Type	Constant Field	Value
public static final String	ALLOSTERIC_PTM	"allosteric post-translational modification"
public static final String	ALLOSTERIC_PTM_MI	"MI:1175"
public static final String	BINDING_SITE	"binding-associated region"
public static final String	BINDING_SITE_MI	"MI:0117"
public static final String	BIOLOGICAL_FEATURE	"biological feature"
public static final String	BIOLOGICAL_FEATURE_MI	"MI:0252"
public static final String	DECREASING_PTM	"decreasing-ptm"
public static final String	DECREASING_PTM_MI	"MI:1223"
public static final String	DIRECT_BINDING	"direct binding region"
public static final String	DIRECT_BINDING_MI	"MI:1125"
public static final String	DISRUPTING_PTM	"disrupting-ptm"
public static final String	DISRUPTING_PTM_MI	"MI:1225"
public static final String	EXPERIMENTAL_FEATURE	"experimental feature"
public static final String	EXPERIMENTAL_FEATURE_MI	"MI:0505"
public static final String	INCREASING_PTM	"increasing-ptm"
public static final String	INCREASING_PTM_MI	"MI:1224"
public static final String	MUTATION	"mutation"
public static final String	MUTATION_MI	"MI:0118"
public static final String	OBSERVED_PTM	"observed ptm"
public static final String	OBSERVED_PTM_MI	"MI:0925"
public static final String	PREREQUISITE_PTM	"prerequisite-ptm"
public static final String	PREREQUISITE_PTM_MI	"MI:0638"
public static final String	RESULTING_CLEAVAGE	"resulting-cleavage"
public static final String	RESULTING_CLEAVAGE_MI	"MI:1233"
public static final String	RESULTING_PTM	"resulting-ptm"
public static final String	RESULTING_PTM_MI	"MI:0639"
public static final String	SUFFICIENT_BINDING	"sufficient binding region"
public static final String	SUFFICIENT_BINDING_MI	"MI:0442"
public static final String	VARIANT	"variant"
public static final String	VARIANT_MI	"MI:1241"

psidev.psi.mi.jami.model.Gene

Modifier and Type	Constant Field	Value
public static final String	GENE	"gene"
public static final String	GENE_MI	"MI:0250"

psidev.psi.mi.jami.model.Interactor

Modifier and Type	Constant Field	Value
public static final String	UNKNOWN_INTERACTOR	"unknown participant"
public static final String	UNKNOWN_INTERACTOR_MI	"MI:0329"

psidev.psi.mi.jami.model.InteractorPool

Modifier and Type	Constant Field	Value
public static final String	CANDIDATE_SET	"candidate set"
public static final String	CANDIDATE_SET_MI	"MI:1305"
public static final String	DEFINED_SET	"defined set"
public static final String	DEFINED_SET_MI	"MI:1307"
public static final String	MOLECULE_SET	"molecule set"
public static final String	MOLECULE_SET_MI	"MI:1304"
public static final String	OPEN_SET	"open set"
public static final String	OPEN_SET_MI	"MI:1306"

psidev.psi.mi.jami.model.ModelledInteraction

Modifier and Type	Constant Field	Value
public static final String	ECO	"evidence ontology"
public static final String	ECO_MI	"MI:1331"

psidev.psi.mi.jami.model.NucleicAcid

Modifier and Type	Constant Field	Value
public static final String	NULCEIC_ACID	"nucleic acid"
public static final String	NULCEIC_ACID_MI	"MI:0318"

psidev.psi.mi.jami.model.Participant<I extends Interaction,F extends Feature>

Modifier and Type	Constant Field	Value
public static final String	ACCEPTOR_ROLE	"acceptor"
public static final String	ACCEPTOR_ROLE_MI	"MI:0919"
public static final String	BAIT_ROLE	"bait"
public static final String	BAIT_ROLE_MI	"MI:0496"
public static final String	DONOR_ROLE	"donor"
public static final String	DONOR_ROLE_MI	"MI:0918"
public static final String	ELECTRON_ACCEPTOR_ROLE	"electron acceptor"
public static final String	ELECTRON_ACCEPTOR_ROLE_MI	"MI:0580"
public static final String	ELECTRON_DONOR_ROLE	"electron donor"
public static final String	ELECTRON_DONOR_ROLE_MI	"MI:0579"
public static final String	ENZYME_REGULATOR_ROLE	"enzyme regulator"
public static final String	ENZYME_REGULATOR_ROLE_MI	"MI:1343"
public static final String	ENZYME_ROLE	"enzyme"
public static final String	ENZYME_ROLE_MI	"MI:0501"
public static final String	ENZYME_TARGET_ROLE	"enzyme target"
public static final String	ENZYME_TARGET_ROLE_MI	"MI:0502"
public static final String	FLUORESCENCE_ACCEPTOR_ROLE	"fluorescence acceptor"
public static final String	FLUORESCENCE_ACCEPTOR_ROLE_MI	"MI:0584"
public static final String	FLUORESCENCE_DONOR_ROLE	"fluorescence donor"
public static final String	FLUORESCENCE_DONOR_ROLE_MI	"MI:0583"
public static final String	INHIBITED	"inhibited"
public static final String	INHIBITED_MI	"MI:0587"
public static final String	INHIBITOR	"inhibitor"
public static final String	INHIBITOR_MI	"MI:0586"
public static final String	NEUTRAL	"neutral component"
public static final String	NEUTRAL_MI	"MI:0497"
public static final String	PHOSPHATE_ACCEPTOR_ROLE	"phosphate acceptor"
public static final String	PHOSPHATE_ACCEPTOR_ROLE_MI	"MI:0843"
public static final String	PHOSPHATE_DONOR_ROLE	"phosphate donor"
public static final String	PHOSPHATE_DONOR_ROLE_MI	"MI:0842"
public static final String	PHOTON_ACCEPTOR_ROLE	"photon acceptor"
public static final String	PHOTON_ACCEPTOR_ROLE_MI	"MI:1085"
public static final String	PHOTON_DONOR_ROLE	"photon donor"
public static final String	PHOTON_DONOR_ROLE_MI	"MI:1084"
public static final String	PREDETERMINED	"predetermined"
public static final String	PREDETERMINED_MI	"MI:0396"
public static final String	PREY	"prey"
public static final String	PREY_MI	"MI:0498"
public static final String	PUTATIVE_SELF_ROLE	"putative self"
public static final String	PUTATIVE_SELF_ROLE_MI	"MI:0898"
public static final String	SELF_ROLE	"self"
public static final String	SELF_ROLE_MI	"MI:0503"
public static final String	SUPPRESSED_GENE_ROLE	"suppressed gene"
public static final String	SUPPRESSED_GENE_ROLE_MI	"MI:0582"
public static final String	SUPPRESSOR_GENE_ROLE	"suppressor gene"
public static final String	SUPPRESSOR_GENE_ROLE_MI	"MI:0581"
public static final String	UNSPECIFIED_ROLE	"unspecified role"
public static final String	UNSPECIFIED_ROLE_MI	"MI:0499"

psidev.psi.mi.jami.model.Polymer

Modifier and Type	Constant Field	Value
public static final String	POLYMER	"biopolymer"
public static final String	POLYMER_MI	"MI:0383"

psidev.psi.mi.jami.model.Position

Modifier and Type	Constant Field	Value
public static final String	C_TERMINAL	"c-terminal"
public static final String	C_TERMINAL_FULL	"c-terminal position"
public static final String	C_TERMINAL_MI	"MI:0334"
public static final String	C_TERMINAL_RANGE	"c-term range"
public static final String	C_TERMINAL_RANGE_FULL	"c-terminal range"
public static final String	C_TERMINAL_RANGE_MI	"MI:1039"
public static final String	CERTAIN	"certain"
public static final String	CERTAIN_FULL	"certain sequence position"
public static final String	CERTAIN_MI	"MI:0335"
public static final String	GREATER_THAN	"greater-than"
public static final String	GREATER_THAN_FULL	"greater-than"
public static final String	GREATER_THAN_MI	"MI:0336"
public static final String	LESS_THAN	"less-than"
public static final String	LESS_THAN_FULL	"less-than"
public static final String	LESS_THAN_MI	"MI:0337"
public static final String	N_TERMINAL	"n-terminal"
public static final String	N_TERMINAL_FULL	"n-terminal position"
public static final String	N_TERMINAL_MI	"MI:0340"
public static final String	N_TERMINAL_RANGE	"n-term range"
public static final String	N_TERMINAL_RANGE_FULL	"n-terminal range"
public static final String	N_TERMINAL_RANGE_MI	"MI:1040"
public static final String	RAGGED_N_TERMINAL	"ragged n-terminus"
public static final String	RAGGED_N_TERMINAL_MI	"MI:0341"
public static final String	RANGE	"range"
public static final String	RANGE_FULL	"range"
public static final String	RANGE_MI	"MI:0338"
public static final String	UNDETERMINED	"undetermined"
public static final String	UNDETERMINED_FULL	"undetermined sequence position"
public static final String	UNDETERMINED_MI	"MI:0339"

psidev.psi.mi.jami.model.Protein

Modifier and Type	Constant Field	Value
public static final String	PEPTIDE	"peptide"
public static final String	PEPTIDE_MI	"MI:0327"
public static final String	PROTEIN	"protein"
public static final String	PROTEIN_MI	"MI:0326"

psidev.psi.mi.jami.model.Range

Modifier and Type	Constant Field	Value
public static final String	C_TERMINAL_POSITION_SYMBOL	"c"
public static final String	FUZZY_POSITION_SYMBOL	".."
public static final String	GREATER_THAN_POSITION_SYMBOL	">"
public static final String	LESS_THAN_POSITION_SYMBOL	"<"
public static final String	N_TERMINAL_POSITION_SYMBOL	"n"
public static final String	POSITION_SEPARATOR	"-"
public static final String	UNDETERMINED_POSITION_SYMBOL	"?"

psidev.psi.mi.jami.model.Xref

Modifier and Type	Constant Field	Value
public static final String	CHAIN_PARENT	"chain-parent"
public static final String	CHAIN_PARENT_MI	"MI:0951"
public static final String	CHEBI	"chebi"
public static final String	CHEBI_MI	"MI:0474"
public static final String	COMPLEX_PORTAL	"complex portal"
public static final String	COMPLEX_PORTAL_MI	"MI:2279"
public static final String	COMPLEX_PRIMARY	"complex-primary"
public static final String	COMPLEX_PRIMARY_MI	"MI:2282"
public static final String	DDBJ_EMBL_GENBANK	"ddbj/embl/genbank"
public static final String	DDBJ_EMBL_GENBANK_MI	"MI:0475"
public static final String	DOI	"doi"
public static final String	DOI_MI	"MI:0574"
public static final String	ENSEMBL	"ensembl"
public static final String	ENSEMBL_GENOMES	"ensemblgenomes"
public static final String	ENSEMBL_GENOMES_MI	"MI:1013"
public static final String	ENSEMBL_MI	"MI:0476"
public static final String	ENTREZ_GENE	"entrezgene/locuslink"
public static final String	ENTREZ_GENE_MI	"MI:0477"
public static final String	GO	"go"
public static final String	GO_MI	"MI:0448"
public static final String	IDENTITY	"identity"
public static final String	IDENTITY_MI	"MI:0356"
public static final String	IMEX	"imex"
public static final String	IMEX_MI	"MI:0670"
public static final String	IMEX_PRIMARY	"imex-primary"
public static final String	IMEX_PRIMARY_MI	"MI:0662"
public static final String	INTACT_MI	"MI:0469"
public static final String	INTERACTOR_SET_QUALIFIER	"set member"
public static final String	INTERACTOR_SET_QUALIFIER_MI	"MI:1341"
public static final String	INTERPRO	"interpro"
public static final String	INTERPRO_MI	"MI:0449"
public static final String	ISOFORM_PARENT	"isoform-parent"
public static final String	ISOFORM_PARENT_MI	"MI:0243"
public static final String	METHOD_REFERENCE	"method reference"
public static final String	METHOD_REFERENCE_MI	"MI:0357"
public static final String	PRIMARY	"primary-reference"
public static final String	PRIMARY_MI	"MI:0358"
public static final String	PUBMED	"pubmed"
public static final String	PUBMED_MI	"MI:0446"
public static final String	REFSEQ	"refseq"
public static final String	REFSEQ_MI	"MI:0481"
public static final String	RESID	"resid"
public static final String	RESID_MI	"MI:0248"
public static final String	SECONDARY	"secondary-ac"
public static final String	SECONDARY_MI	"MI:0360"
public static final String	SEE_ALSO	"see-also"
public static final String	SEE_ALSO_MI	"MI:0361"
public static final String	SO	"so"
public static final String	SO_MI	"MI:0601"
public static final String	UNIPROTKB	"uniprotkb"
public static final String	UNIPROTKB_MI	"MI:0486"
public static final String	UNIPROTKB_SWISSPROT	"swiss-prot"
public static final String	UNIPROTKB_SWISSPROT_MI	"MI:1098"
public static final String	UNIPROTKB_TREMBL	"trembl"
public static final String	UNIPROTKB_TREMBL_MI	"MI:1099"

psidev.psi.mi.jami.tab.extension.factory.options.MitabWriterOptions

Modifier and Type	Constant Field	Value
public static final String	MITAB_EXTENDED_OPTION	"mitab_extended_key"
public static final String	MITAB_HEADER_OPTION	"mitab_header_key"
public static final String	MITAB_VERSION_OPTION	"mitab_version_key"

psidev.psi.mi.jami.tab.io.parser.JavaCharStream

Modifier and Type	Constant Field	Value
public static final boolean	staticFlag	false

psidev.psi.mi.jami.tab.io.parser.MitabLineParserConstants

Modifier and Type	Constant Field	Value
public static final int	CLOSE_PAREN	9
public static final int	COLON	10
public static final int	COLUMN_SEPARATOR	6
public static final int	COMMENT	4
public static final int	DASH	11
public static final int	DEFAULT	0
public static final int	EOF	0
public static final int	FIELD_SEPARATOR	5
public static final int	LINE_SEPARATOR	7
public static final int	OPEN_PAREN	8
public static final int	QUOTED_STRING	12
public static final int	RANGE_SEPARATOR	3
public static final int	UNRESERVED_STRING	13

psidev.psi.mi.jami.tab.io.parser.SimpleCharStream

Modifier and Type	Constant Field	Value
public static final boolean	staticFlag	false

psidev.psi.mi.jami.tab.utils.MitabUtils

Modifier and Type	Constant Field	Value
public static final String	AUTHOR_SUFFIX	" et al."
public static final String	COLUMN_SEPARATOR	"\t"
public static final String	COMMENT_PREFIX	"#"
public static final String	DISPLAY_LONG	"display_long"
public static final String	DISPLAY_SHORT	"display_short"
public static final String	EMPTY_COLUMN	"-"
public static final String	FIELD_SEPARATOR	"|"
public static final String	RANGE_SEPARATOR	","
public static final String	SHORTLABEL	"shortlabel"
public static final String	TAXID	"taxid"
public static final String	UNKNOWN_DATABASE	"unknown"
public static final String	UNKNOWN_ID	"unknown"
public static final String	UNKNOWN_NAME	"unspecified name"
public static final String	UNKNOWN_TYPE	"unknown"
public static final String	XREF_SEPARATOR	":"

psidev.psi.mi.jami.utils.checksum.Base64

Modifier and Type	Constant Field	Value
public static final int	DECODE	0
public static final int	DONT_BREAK_LINES	8
public static final int	ENCODE	1
public static final int	GZIP	2
public static final int	NO_OPTIONS	0
public static final int	ORDERED	32
public static final int	URL_SAFE	16

psidev.psi.mi.jami.xml.model.extension.datasource.AbstractPsiXmlStream<T extends Interaction>

Modifier and Type	Constant Field	Value
public static final String	SCHEMA_FEATURE	"http://apache.org/xml/features/validation/schema"
public static final String	VALIDATION_FEATURE	"http://xml.org/sax/features/validation"

psidev.psi.mi.jami.xml.model.extension.factory.options.PsiXmlDataSourceOptions

Modifier and Type	Constant Field	Value
public static final String	ELEMENT_WITH_ID_CACHE_OPTION	"element_id_cache_key"

psidev.psi.mi.jami.xml.model.extension.factory.options.PsiXmlWriterOptions

Modifier and Type	Constant Field	Value
public static final String	COMPACT_XML_AVAILABILITY_SET_OPTION	"compact_xml_availability_set_key"
public static final String	COMPACT_XML_EXPERIMENT_SET_OPTION	"compact_xml_experiment_set_key"
public static final String	COMPACT_XML_INTERACTOR_SET_OPTION	"compact_xml_interactor_set_key"
public static final String	DEFAULT_RELEASE_DATE_OPTION	"default_release_date_key"
public static final String	DEFAULT_SOURCE_OPTION	"default_source_key"
public static final String	ELEMENT_WITH_ID_CACHE_OPTION	"element_id_cache_key"
public static final String	WRITE_COMPLEX_AS_INTERACTOR_OPTION	"write_complex_as_interactor_key"
public static final String	XML_ENTRY_ATTRIBUTES_OPTION	"xml25_entry_attributes_key"
public static final String	XML_EXTENDED_OPTION	"xml25_extended_key"
public static final String	XML_INTERACTION_SET_OPTION	"xml_interaction_set_key"
public static final String	XML_NAMES_OPTION	"xml25_names_key"
public static final String	XML_TYPE_OPTION	"xml25_type_key"
public static final String	XML_VERSION_OPTION	"xml_version_key"

psidev.psi.mi.jami.xml.utils.PsiXmlUtils

Modifier and Type	Constant Field	Value
public static final String	ABSTRACT_INTERACTION_TAG	"abstractInteraction"
public static final String	ATTRIBUTE_TAG	"attribute"
public static final String	ATTRIBUTELIST_TAG	"attributeList"
public static final String	AVAILABILITY_TAG	"availability"
public static final String	AVAILABILITYLIST_TAG	"availabilityList"
public static final String	ENTRY_TAG	"entry"
public static final String	ENTRYSET_TAG	"entrySet"
public static final String	EXPERIMENT_TAG	"experimentDescription"
public static final String	EXPERIMENTLIST_TAG	"experimentList"
public static final String	INTERACTION_TAG	"interaction"
public static final String	INTERACTIONLIST_TAG	"interactionList"
public static final String	INTERACTOR_TAG	"interactor"
public static final String	INTERACTORLIST_TAG	"interactorList"
public static final String	LEVEL_ATTRIBUTE	"level"
public static final String	LINE_BREAK	"\n"
public static final String	MINOR_VERSION_ATTRIBUTE	"minorVersion"
public static final String	PSI_SCHEMA_253_LOCATION	"net:sf:psidev:mi https://raw.githubusercontent.com/HUPO-PSI/miXML/master/2.5/src/MIF253.xsd"
public static final String	PSI_SCHEMA_254_LOCATION	"http://psi.hupo.org/mi/mif https://raw.githubusercontent.com/HUPO-PSI/miXML/master/2.5/src/MIF254.xsd"
public static final String	PSI_SCHEMA_300_LOCATION	"http://psi.hupo.org/mi/mif300 https://raw.githubusercontent.com/HUPO-PSI/miXML/master/3.0/src/MIF300.xsd"
public static final String	SCHEMA_LOCATION_ATTRIBUTE	"schemaLocation"
public static final String	SOURCE_TAG	"source"
public static final String	STOICHIOMETRY_PREFIX	"stoichiometry: "
public static final String	UNSPECIFIED	"unspecified"
public static final String	VERSION_ATTRIBUTE	"version"
public static final int	XML_BUFFER_SIZE	2048
public static final String	XML_SCHEMA	"http://www.w3.org/2001/XMLSchema-instance"
public static final String	XML_SCHEMA_PREFIX	"xsi"
public static final String	Xml253_NAMESPACE_URI	"net:sf:psidev:mi"
public static final String	Xml254_NAMESPACE_URI	"http://psi.hupo.org/mi/mif"
public static final String	Xml300_NAMESPACE_URI	"http://psi.hupo.org/mi/mif300"