PubDictionaries

Text annotation

Demo

Min Length	Max Length	Threshold	Abbreviation	Longest	Superfluous	Verbose

Dictionary Selection

Selected		Unselected
ACGG-DB-GGDB ACGG-DB-LfDB ACTI1_YXZ ACTI2_YXZ ACTI_CY addFirstAuthorsDisease Addition_for_LitCoin_chemical Addition_for_LitCoin_Disease Addition_for_LitCoin_Disease_2 AGACQA agrold Allie-Literal-Pairs Allie-Longtform-Literal-URI-Pairs Allie-Shortform-Literal-URI-Pairs ANAT1_YXZ ANAT2_YXZ ANAT_CY Bioverb blah4-bth BLAH6-GNI-DICTIONARY BLAH6test cancer-and-gene Cell_line Cellosaurus Cellosaurus_v33 Cellosaurus_v35 CHEBI CHEBI-2020-03-31 CHEBI_tmp CHEM1_YXZ CHEM2_YXZ CHEM_CY CLO-20190210 CLO-20211022 colil_dic colil_pred_dic CONC1_YXZ CONC2_YXZ CONC_CY Context Annotation covid19drugs Covid19_manual_annotation covid19-sample demo-Animals demo-Food demo-Persons demo-Relations demo-Tools DEVI1_YXZ DEVI2_YXZ DEVI_CY Disease_Mesh_All Diseasome-QALD DISO1_YXZ DISO2_YXZ DISO_CY DRON-2020-04-05 DrugBank-Bio2RDF-r3 DrugBank-QALD Drug_Test EBI_biome_list EFO-cultured_cells enzyme Equipment_Supplies Erin_dic Firmness FirstAuthorDictionay FirstAuthorsDrugChemicals FirstAuthorsPlants FirstAuthorsUniProt FirstAuthorUnknownDisease FMA-PAE Fragaria ananassa disease Fragaria_ananassa_genes Fragaria_ananassa_nuccore GENE1_YXZ GENE2_YXZ GENE_CY Glycan-Motif Glycan-Motif-Image GlycoEpitope GlycoEpitope-DBCLS glycogenes glycogenes-20190927 glyconavi-glycan-abbreviation glyconavi-glycan-name glyconavi-glycan-subtype glyconavi-SNFG-MS glyconavi-SNFG-MS-Abbreviation glycoprotein-name GlyTouCan_IDs glytoucan-iupac GlyTouCan-IUPAC_condensed GlyTouCan-iupacX GO-Bio2RDF-r3 GO-BP GO-CC GO-MF HGNC-Bio2RDF-r3 HP_2020-02-27 HP_DBCLS HP_Garvan HPO-japanese-alpha-18Oct2017 HP-PA HP_Subset_Garvan human-UniProt IDO-2020-01-06 inforMED_test JapaneseHistoryTest KCB_DB_test KEGG-Bio2RDF-r3 Life Science Dictionary (CC BY-ND) LIVB1_YXZ LIVB2_YXZ LIVB_CY lsdb MAT MAT0 MedDRA-Investigations MENA_metagenomics_hosts MENA_metagenomics_hosts_v1 MeSH2022Chemical MeSH2022Chemical_descriptor MeSH2022_chemical_not_gene_or_protein MeSH2022Disease MeSH2022MentalDisorder Mesh_All_FN MeSH_by_wikidata_English_test MeSH_by_wikidata_English_with_aliases MeSH_by_wikidata_Japanese_test MeSH_by_wikidata_Japanese_with_aliases MeSH_LitCovid_Japanese_Curated Mondo MONDO Mondo_2019_Kim MONDO_bioportal_prefferred_name MONDO_label_synonym MONDO_merge motifGlyTouCanID MutationRegExp ncats-experimental NCBIGene-Human-NER NCBIGene-NER ncbi_taxon NCBITaxon NCBITAXON NCBITaxon4LC NCBITAXON-Mammalia-2019-11-04 NCBITAXON-Viruses-2019-11-04 NGLY1-deficiency nothing OBJC1_YXZ OBJC2_YXZ OBJC_CY oldEquipment_Supplies OMIM-Bio2RDF-r3 open-tggates-test ORGA1_YXZ ORGA2_YXZ ORGA_CY OryzaGeneName_MSU OryzaGeneName_MSU_symbols OryzaGeneName_Oryzabase OryzaGeneName_Oryzabase_Symbols OryzaGeneName_RAPDB OryzaGeneName_RAPDB_symbols OryzaGeneNames OryzaGeneName_UniProt OryzaGeneName_UNIPROT_symbols PD-ORYZAGP2022 PE_short pg_trait PHEN1_YXZ PHEN2_YXZ PHEN_CY PHYS1_YXZ PHYS2_YXZ PHYS_CY Preeclampsia preeclampsia_genes preeclampsia_hgnc preeclampsia-test PROC1_YXZ PROC2_YXZ PROC_CY PSI-MS-4_1_100 PTO-all PTO-exact QTL-test Regulation Regulation_new_3 Regulation_not_yet SIDER-Bio2RDF-r3 SIDER-QALD silkworm_phenotype Taxonomy-Bio2RDF-r3 test Test test432 testdic Test_Dic Test_Economics_L test_hpo_ja test-jp testtesttest togotv_test TweetsDictionary UBERON-AE uniprot-accession-identifiers-org UniProt-Covid19 UniProt-hGene www		ACGG-DB-GGDB ACGG-DB-LfDB ACTI1_YXZ ACTI2_YXZ ACTI_CY addFirstAuthorsDisease Addition_for_LitCoin_chemical Addition_for_LitCoin_Disease Addition_for_LitCoin_Disease_2 AGACQA agrold Allie-Literal-Pairs Allie-Longtform-Literal-URI-Pairs Allie-Shortform-Literal-URI-Pairs ANAT1_YXZ ANAT2_YXZ ANAT_CY Bioverb blah4-bth BLAH6-GNI-DICTIONARY BLAH6test cancer-and-gene Cell_line Cellosaurus Cellosaurus_v33 Cellosaurus_v35 CHEBI CHEBI-2020-03-31 CHEBI_tmp CHEM1_YXZ CHEM2_YXZ CHEM_CY CLO-20190210 CLO-20211022 colil_dic colil_pred_dic CONC1_YXZ CONC2_YXZ CONC_CY Context Annotation covid19drugs Covid19_manual_annotation covid19-sample demo-Animals demo-Food demo-Persons demo-Relations demo-Tools DEVI1_YXZ DEVI2_YXZ DEVI_CY Disease_Mesh_All Diseasome-QALD DISO1_YXZ DISO2_YXZ DISO_CY DRON-2020-04-05 DrugBank-Bio2RDF-r3 DrugBank-QALD Drug_Test EBI_biome_list EFO-cultured_cells enzyme Equipment_Supplies Erin_dic Firmness FirstAuthorDictionay FirstAuthorsDrugChemicals FirstAuthorsPlants FirstAuthorsUniProt FirstAuthorUnknownDisease FMA-PAE Fragaria ananassa disease Fragaria_ananassa_genes Fragaria_ananassa_nuccore GENE1_YXZ GENE2_YXZ GENE_CY Glycan-Motif Glycan-Motif-Image GlycoEpitope GlycoEpitope-DBCLS glycogenes glycogenes-20190927 glyconavi-glycan-abbreviation glyconavi-glycan-name glyconavi-glycan-subtype glyconavi-SNFG-MS glyconavi-SNFG-MS-Abbreviation glycoprotein-name GlyTouCan_IDs glytoucan-iupac GlyTouCan-IUPAC_condensed GlyTouCan-iupacX GO-Bio2RDF-r3 GO-BP GO-CC GO-MF HGNC-Bio2RDF-r3 HP_2020-02-27 HP_DBCLS HP_Garvan HPO-japanese-alpha-18Oct2017 HP-PA HP_Subset_Garvan human-UniProt IDO-2020-01-06 inforMED_test JapaneseHistoryTest KCB_DB_test KEGG-Bio2RDF-r3 Life Science Dictionary (CC BY-ND) LIVB1_YXZ LIVB2_YXZ LIVB_CY lsdb MAT MAT0 MedDRA-Investigations MENA_metagenomics_hosts MENA_metagenomics_hosts_v1 MeSH2022Chemical MeSH2022Chemical_descriptor MeSH2022_chemical_not_gene_or_protein MeSH2022Disease MeSH2022MentalDisorder Mesh_All_FN MeSH_by_wikidata_English_test MeSH_by_wikidata_English_with_aliases MeSH_by_wikidata_Japanese_test MeSH_by_wikidata_Japanese_with_aliases MeSH_LitCovid_Japanese_Curated Mondo MONDO Mondo_2019_Kim MONDO_bioportal_prefferred_name MONDO_label_synonym MONDO_merge motifGlyTouCanID MutationRegExp ncats-experimental NCBIGene-Human-NER NCBIGene-NER ncbi_taxon NCBITaxon NCBITAXON NCBITaxon4LC NCBITAXON-Mammalia-2019-11-04 NCBITAXON-Viruses-2019-11-04 NGLY1-deficiency nothing OBJC1_YXZ OBJC2_YXZ OBJC_CY oldEquipment_Supplies OMIM-Bio2RDF-r3 open-tggates-test ORGA1_YXZ ORGA2_YXZ ORGA_CY OryzaGeneName_MSU OryzaGeneName_MSU_symbols OryzaGeneName_Oryzabase OryzaGeneName_Oryzabase_Symbols OryzaGeneName_RAPDB OryzaGeneName_RAPDB_symbols OryzaGeneNames OryzaGeneName_UniProt OryzaGeneName_UNIPROT_symbols PD-ORYZAGP2022 PE_short pg_trait PHEN1_YXZ PHEN2_YXZ PHEN_CY PHYS1_YXZ PHYS2_YXZ PHYS_CY Preeclampsia preeclampsia_genes preeclampsia_hgnc preeclampsia-test PROC1_YXZ PROC2_YXZ PROC_CY PSI-MS-4_1_100 PTO-all PTO-exact QTL-test Regulation Regulation_new_3 Regulation_not_yet SIDER-Bio2RDF-r3 SIDER-QALD silkworm_phenotype Taxonomy-Bio2RDF-r3 test Test test432 testdic Test_Dic Test_Economics_L test_hpo_ja test-jp testtesttest togotv_test TweetsDictionary UBERON-AE uniprot-accession-identifiers-org UniProt-Covid19 UniProt-hGene www

At least one dictionary has to be selected.

REST API for annotation

GET|POST

paste it to PubAnnotation

Example cURL command

1	GET
2	POST
3	POST
4	POST

REST API for batch annotation

POST

Example cURL command

1	POST