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-0,0 +1,98 @@ + + + + + +%NCBI_Entity_module; + + +%EMBL_General_module; + + +%GenBank_General_module; + + +%MMDB_module; + + +%MMDB_Chemical_graph_module; + + +%MMDB_Features_module; + + +%MMDB_Structural_model_module; + + +%NCBI_Biblio_module; + + +%NCBI_BioSource_module; + + +%NCBI_Gene_module; + + +%NCBI_General_module; + + +%NCBI_Medline_module; + + +%NCBI_Organism_module; + + +%NCBI_Protein_module; + + +%NCBI_Pub_module; + + +%NCBI_RNA_module; + + +%NCBI_Rsite_module; + + +%NCBI_SeqTable_module; + + +%NCBI_Seqalign_module; + + +%NCBI_Seqfeat_module; + + +%NCBI_Seqloc_module; + + +%NCBI_Seqres_module; + + +%NCBI_Sequence_module; + + +%NCBI_TxInit_module; + + +%NCBI_Variation_module; + + +%PDB_General_module; + + +%PIR_General_module; + + +%PRF_General_module; + + +%SP_General_module; diff --git a/dtd/MMDB_Structural_model.mod.dtd b/dtd/MMDB_Structural_model.mod.dtd new file mode 100644 index 0000000..aa9f16c --- /dev/null +++ b/dtd/MMDB_Structural_model.mod.dtd @@ -0,0 +1,676 @@ + 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b/dtd/NCBI_Access.mod.dtd @@ -0,0 +1,49 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + diff --git a/dtd/NCBI_Biblio.dtd b/dtd/NCBI_Biblio.dtd new file mode 100644 index 0000000..17edc09 --- /dev/null +++ b/dtd/NCBI_Biblio.dtd @@ -0,0 +1,20 @@ + + + + + +%NCBI_Entity_module; + + +%NCBI_Biblio_module; + + +%NCBI_General_module; diff --git a/dtd/NCBI_Biblio.mod.dtd b/dtd/NCBI_Biblio.mod.dtd new file mode 100644 index 0000000..e0b7e1d --- /dev/null +++ b/dtd/NCBI_Biblio.mod.dtd @@ -0,0 +1,690 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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diff --git a/dtd/NCBI_BioTree.dtd b/dtd/NCBI_BioTree.dtd new file mode 100644 index 0000000..26ba5d9 --- /dev/null +++ b/dtd/NCBI_BioTree.dtd @@ -0,0 +1,17 @@ + + + + + +%NCBI_Entity_module; + + +%NCBI_BioTree_module; diff --git a/dtd/NCBI_BioTree.mod.dtd b/dtd/NCBI_BioTree.mod.dtd new file mode 100644 index 0000000..7a2ad1a --- /dev/null +++ b/dtd/NCBI_BioTree.mod.dtd @@ -0,0 +1,109 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + diff --git a/dtd/NCBI_Blast4.dtd b/dtd/NCBI_Blast4.dtd new file mode 100644 index 0000000..24437c5 --- /dev/null +++ b/dtd/NCBI_Blast4.dtd @@ -0,0 +1,95 @@ + + + + + +%NCBI_Entity_module; + + +%EMBL_General_module; + + +%GenBank_General_module; + + +%NCBI_Biblio_module; + + +%NCBI_BioSource_module; + + +%NCBI_Blast4_module; + + +%NCBI_Gene_module; + + +%NCBI_General_module; + + +%NCBI_Medline_module; + + +%NCBI_Organism_module; + + +%NCBI_Protein_module; + + +%NCBI_Pub_module; + + +%NCBI_RNA_module; + + +%NCBI_Rsite_module; + + +%NCBI_ScoreMat_module; + + +%NCBI_SeqTable_module; + + +%NCBI_Seqalign_module; + + +%NCBI_Seqfeat_module; + + +%NCBI_Seqloc_module; + + +%NCBI_Seqres_module; + + +%NCBI_Seqset_module; + + +%NCBI_Sequence_module; + + +%NCBI_TxInit_module; + + +%NCBI_Variation_module; + + +%PDB_General_module; + + +%PIR_General_module; + + +%PRF_General_module; + + +%SP_General_module; diff --git a/dtd/NCBI_Blast4.mod.dtd b/dtd/NCBI_Blast4.mod.dtd new file mode 100644 index 0000000..f001a47 --- /dev/null +++ b/dtd/NCBI_Blast4.mod.dtd @@ -0,0 +1,1498 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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+ + + + + + + + + + + + + diff --git a/dtd/NCBI_BlastDL.dtd b/dtd/NCBI_BlastDL.dtd new file mode 100644 index 0000000..451e782 --- /dev/null +++ b/dtd/NCBI_BlastDL.dtd @@ -0,0 +1,89 @@ + + + + + +%NCBI_Entity_module; + + +%EMBL_General_module; + + +%GenBank_General_module; + + +%NCBI_Biblio_module; + + +%NCBI_BioSource_module; + + +%NCBI_BlastDL_module; + + +%NCBI_Gene_module; + + +%NCBI_General_module; + + +%NCBI_Medline_module; + + +%NCBI_Organism_module; + + +%NCBI_Protein_module; + + +%NCBI_Pub_module; + + +%NCBI_RNA_module; + + +%NCBI_Rsite_module; + + +%NCBI_SeqTable_module; + + +%NCBI_Seqalign_module; + + +%NCBI_Seqfeat_module; + + +%NCBI_Seqloc_module; + + +%NCBI_Seqres_module; + + +%NCBI_Sequence_module; + + +%NCBI_TxInit_module; + + +%NCBI_Variation_module; + + +%PDB_General_module; + + +%PIR_General_module; + + +%PRF_General_module; + + +%SP_General_module; diff --git a/dtd/NCBI_BlastDL.mod.dtd b/dtd/NCBI_BlastDL.mod.dtd new file mode 100644 index 0000000..78a99bb --- /dev/null +++ b/dtd/NCBI_BlastDL.mod.dtd @@ -0,0 +1,138 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + diff --git a/dtd/NCBI_BlastOutput.dtd b/dtd/NCBI_BlastOutput.dtd new file mode 100644 index 0000000..307176a --- /dev/null +++ b/dtd/NCBI_BlastOutput.dtd @@ -0,0 +1,17 @@ + + + + + +%NCBI_Entity_module; + + +%NCBI_BlastOutput_module; diff --git a/dtd/NCBI_BlastOutput.mod.dtd b/dtd/NCBI_BlastOutput.mod.dtd new file mode 100644 index 0000000..7b0f47f --- /dev/null +++ b/dtd/NCBI_BlastOutput.mod.dtd @@ -0,0 +1,273 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + diff --git a/dtd/NCBI_Cdd.dtd b/dtd/NCBI_Cdd.dtd new file mode 100644 index 0000000..b2d06ad --- /dev/null +++ b/dtd/NCBI_Cdd.dtd @@ -0,0 +1,110 @@ + + + + + +%NCBI_Entity_module; + + +%EMBL_General_module; + + +%GenBank_General_module; + + +%MMDB_module; + + +%MMDB_Chemical_graph_module; + + +%MMDB_Features_module; + + +%MMDB_Structural_model_module; + + +%NCBI_Biblio_module; + + +%NCBI_BioSource_module; + + +%NCBI_Cdd_module; + + +%NCBI_Cn3d_module; + + +%NCBI_Gene_module; + + +%NCBI_General_module; + + +%NCBI_Medline_module; + + +%NCBI_Organism_module; + + +%NCBI_Protein_module; + + +%NCBI_Pub_module; + + +%NCBI_RNA_module; + + +%NCBI_Rsite_module; + + +%NCBI_ScoreMat_module; + + +%NCBI_SeqTable_module; + + +%NCBI_Seqalign_module; + + +%NCBI_Seqfeat_module; + + +%NCBI_Seqloc_module; + + +%NCBI_Seqres_module; + + +%NCBI_Seqset_module; + + +%NCBI_Sequence_module; + + +%NCBI_TxInit_module; + + +%NCBI_Variation_module; + + +%PDB_General_module; + + +%PIR_General_module; + + +%PRF_General_module; + + +%SP_General_module; diff --git a/dtd/NCBI_Cdd.mod.dtd b/dtd/NCBI_Cdd.mod.dtd new file mode 100644 index 0000000..7cf68d6 --- /dev/null +++ b/dtd/NCBI_Cdd.mod.dtd @@ -0,0 +1,1088 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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+ +%NCBI_Rsite_module; + + +%NCBI_SeqTable_module; + + +%NCBI_Seqalign_module; + + +%NCBI_Seqfeat_module; + + +%NCBI_Seqloc_module; + + +%NCBI_Seqres_module; + + +%NCBI_Sequence_module; + + +%NCBI_TxInit_module; + + +%NCBI_Variation_module; + + +%PDB_General_module; + + +%PIR_General_module; + + +%PRF_General_module; + + +%SP_General_module; diff --git a/dtd/NCBI_Cn3d.mod.dtd b/dtd/NCBI_Cn3d.mod.dtd new file mode 100644 index 0000000..16a815f --- /dev/null +++ b/dtd/NCBI_Cn3d.mod.dtd @@ -0,0 +1,534 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + diff --git a/dtd/NCBI_Entity.mod.dtd b/dtd/NCBI_Entity.mod.dtd new file mode 100644 index 0000000..3919c3e --- /dev/null +++ b/dtd/NCBI_Entity.mod.dtd @@ -0,0 +1,13 @@ + + + + + + + + + + + + + diff --git a/dtd/NCBI_Entrez2.dtd b/dtd/NCBI_Entrez2.dtd new file mode 100644 index 0000000..a08a907 --- /dev/null +++ b/dtd/NCBI_Entrez2.dtd @@ -0,0 +1,17 @@ + + + + + +%NCBI_Entity_module; + + +%NCBI_Entrez2_module; diff --git a/dtd/NCBI_Entrez2.mod.dtd b/dtd/NCBI_Entrez2.mod.dtd new file mode 100644 index 0000000..5eb72c9 --- /dev/null +++ b/dtd/NCBI_Entrez2.mod.dtd @@ -0,0 +1,747 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + diff --git a/dtd/NCBI_Entrezgene.dtd b/dtd/NCBI_Entrezgene.dtd new file mode 100644 index 0000000..36e206f --- /dev/null +++ b/dtd/NCBI_Entrezgene.dtd @@ -0,0 +1,89 @@ + + + + + +%NCBI_Entity_module; + + +%EMBL_General_module; + + +%GenBank_General_module; + + +%NCBI_Biblio_module; + + +%NCBI_BioSource_module; + + +%NCBI_Entrezgene_module; + + +%NCBI_Gene_module; + + +%NCBI_General_module; + + +%NCBI_Medline_module; + + +%NCBI_Organism_module; + + +%NCBI_Protein_module; + + +%NCBI_Pub_module; + + +%NCBI_RNA_module; + + +%NCBI_Rsite_module; + + +%NCBI_SeqTable_module; + + +%NCBI_Seqalign_module; + + +%NCBI_Seqfeat_module; + + +%NCBI_Seqloc_module; + + +%NCBI_Seqres_module; + + +%NCBI_Sequence_module; + + +%NCBI_TxInit_module; + + +%NCBI_Variation_module; + + +%PDB_General_module; + + +%PIR_General_module; + + +%PRF_General_module; + + +%SP_General_module; diff --git a/dtd/NCBI_Entrezgene.mod.dtd b/dtd/NCBI_Entrezgene.mod.dtd new file mode 100644 index 0000000..c75d32f --- /dev/null +++ b/dtd/NCBI_Entrezgene.mod.dtd @@ -0,0 +1,394 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + diff --git a/dtd/NCBI_FeatDef.dtd b/dtd/NCBI_FeatDef.dtd new file mode 100644 index 0000000..a3ce559 --- /dev/null +++ b/dtd/NCBI_FeatDef.dtd @@ -0,0 +1,17 @@ + + + + + +%NCBI_Entity_module; + + +%NCBI_FeatDef_module; diff --git a/dtd/NCBI_FeatDef.mod.dtd b/dtd/NCBI_FeatDef.mod.dtd new file mode 100644 index 0000000..65fbf90 --- /dev/null +++ b/dtd/NCBI_FeatDef.mod.dtd @@ -0,0 +1,97 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + diff --git a/dtd/NCBI_GBSeq.dtd b/dtd/NCBI_GBSeq.dtd new file mode 100644 index 0000000..d317e96 --- /dev/null +++ b/dtd/NCBI_GBSeq.dtd @@ -0,0 +1,17 @@ + + + + + +%NCBI_Entity_module; + + +%NCBI_GBSeq_module; diff --git a/dtd/NCBI_GBSeq.mod.dtd b/dtd/NCBI_GBSeq.mod.dtd new file mode 100644 index 0000000..95be4f3 --- /dev/null +++ b/dtd/NCBI_GBSeq.mod.dtd @@ -0,0 +1,407 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + diff --git a/dtd/NCBI_Gene.dtd b/dtd/NCBI_Gene.dtd new file mode 100644 index 0000000..cd6d122 --- /dev/null +++ b/dtd/NCBI_Gene.dtd @@ -0,0 +1,20 @@ + + + + + +%NCBI_Entity_module; + + +%NCBI_Gene_module; + + +%NCBI_General_module; diff --git a/dtd/NCBI_Gene.mod.dtd b/dtd/NCBI_Gene.mod.dtd new file mode 100644 index 0000000..be703af --- /dev/null +++ b/dtd/NCBI_Gene.mod.dtd @@ -0,0 +1,97 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + diff --git a/dtd/NCBI_General.dtd b/dtd/NCBI_General.dtd new file mode 100644 index 0000000..a8bb6c1 --- /dev/null +++ b/dtd/NCBI_General.dtd @@ -0,0 +1,17 @@ + + + + + +%NCBI_Entity_module; + + +%NCBI_General_module; diff --git a/dtd/NCBI_General.mod.dtd b/dtd/NCBI_General.mod.dtd new file mode 100644 index 0000000..c573ca5 --- /dev/null +++ b/dtd/NCBI_General.mod.dtd @@ -0,0 +1,333 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + diff --git a/dtd/NCBI_ID1Access.dtd b/dtd/NCBI_ID1Access.dtd new file mode 100644 index 0000000..8e57ced --- /dev/null +++ b/dtd/NCBI_ID1Access.dtd @@ -0,0 +1,92 @@ + + + + + +%NCBI_Entity_module; + + +%EMBL_General_module; + + +%GenBank_General_module; + + +%NCBI_Biblio_module; + + +%NCBI_BioSource_module; + + +%NCBI_Gene_module; + + +%NCBI_General_module; + + +%NCBI_ID1Access_module; + + +%NCBI_Medline_module; + + +%NCBI_Organism_module; + + +%NCBI_Protein_module; + + +%NCBI_Pub_module; + + +%NCBI_RNA_module; + + +%NCBI_Rsite_module; + + +%NCBI_SeqTable_module; + + +%NCBI_Seqalign_module; + + +%NCBI_Seqfeat_module; + + +%NCBI_Seqloc_module; + + +%NCBI_Seqres_module; + + +%NCBI_Seqset_module; + + +%NCBI_Sequence_module; + + +%NCBI_TxInit_module; + + +%NCBI_Variation_module; + + +%PDB_General_module; + + +%PIR_General_module; + + +%PRF_General_module; + + +%SP_General_module; diff --git a/dtd/NCBI_ID1Access.mod.dtd b/dtd/NCBI_ID1Access.mod.dtd new file mode 100644 index 0000000..b489907 --- /dev/null +++ b/dtd/NCBI_ID1Access.mod.dtd @@ -0,0 +1,218 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + diff --git a/dtd/NCBI_ID2Access.dtd b/dtd/NCBI_ID2Access.dtd new file mode 100644 index 0000000..4adbfa5 --- /dev/null +++ b/dtd/NCBI_ID2Access.dtd @@ -0,0 +1,95 @@ + + + + + +%NCBI_Entity_module; + + +%EMBL_General_module; + + +%GenBank_General_module; + + +%NCBI_Biblio_module; + + +%NCBI_BioSource_module; + + +%NCBI_Gene_module; + + +%NCBI_General_module; + + +%NCBI_ID2Access_module; + + +%NCBI_Medline_module; + + +%NCBI_Organism_module; + + +%NCBI_Protein_module; + + +%NCBI_Pub_module; + + +%NCBI_RNA_module; + + +%NCBI_Rsite_module; + + +%NCBI_Seq_split_module; + + +%NCBI_SeqTable_module; + + +%NCBI_Seqalign_module; + + +%NCBI_Seqfeat_module; + + +%NCBI_Seqloc_module; + + +%NCBI_Seqres_module; + + +%NCBI_Seqset_module; + + +%NCBI_Sequence_module; + + +%NCBI_TxInit_module; + + +%NCBI_Variation_module; + + +%PDB_General_module; + + +%PIR_General_module; + + +%PRF_General_module; + + +%SP_General_module; diff --git a/dtd/NCBI_ID2Access.mod.dtd b/dtd/NCBI_ID2Access.mod.dtd new file mode 100644 index 0000000..5d5ecf7 --- /dev/null +++ b/dtd/NCBI_ID2Access.mod.dtd @@ -0,0 +1,759 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + diff --git a/dtd/NCBI_MedArchive.dtd b/dtd/NCBI_MedArchive.dtd new file mode 100644 index 0000000..1082302 --- /dev/null +++ b/dtd/NCBI_MedArchive.dtd @@ -0,0 +1,35 @@ + + + + + +%NCBI_Entity_module; + + +%NCBI_Biblio_module; + + +%NCBI_General_module; + + +%NCBI_MedArchive_module; + + +%NCBI_Medlars_module; + + +%NCBI_Medline_module; + + +%NCBI_Pub_module; + + +%NCBI_PubMed_module; diff --git a/dtd/NCBI_MedArchive.mod.dtd b/dtd/NCBI_MedArchive.mod.dtd new file mode 100644 index 0000000..b4c2701 --- /dev/null +++ b/dtd/NCBI_MedArchive.mod.dtd @@ -0,0 +1,271 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + diff --git a/dtd/NCBI_Medlars.dtd b/dtd/NCBI_Medlars.dtd new file mode 100644 index 0000000..6d1410c --- /dev/null +++ b/dtd/NCBI_Medlars.dtd @@ -0,0 +1,23 @@ + + + + + +%NCBI_Entity_module; + + +%NCBI_Biblio_module; + + +%NCBI_General_module; + + +%NCBI_Medlars_module; diff --git a/dtd/NCBI_Medlars.mod.dtd b/dtd/NCBI_Medlars.mod.dtd new file mode 100644 index 0000000..cb8d48a --- /dev/null +++ b/dtd/NCBI_Medlars.mod.dtd @@ -0,0 +1,58 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + diff --git a/dtd/NCBI_Medline.dtd b/dtd/NCBI_Medline.dtd new file mode 100644 index 0000000..9495345 --- /dev/null +++ b/dtd/NCBI_Medline.dtd @@ -0,0 +1,23 @@ + + + + + +%NCBI_Entity_module; + + +%NCBI_Biblio_module; + + +%NCBI_General_module; + + +%NCBI_Medline_module; diff --git a/dtd/NCBI_Medline.mod.dtd b/dtd/NCBI_Medline.mod.dtd new file mode 100644 index 0000000..b05a78e --- /dev/null +++ b/dtd/NCBI_Medline.mod.dtd @@ -0,0 +1,245 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + diff --git a/dtd/NCBI_Mim.dtd b/dtd/NCBI_Mim.dtd new file mode 100644 index 0000000..7dc862b --- /dev/null +++ b/dtd/NCBI_Mim.dtd @@ -0,0 +1,17 @@ + + + + + +%NCBI_Entity_module; + + +%NCBI_Mim_module; diff --git a/dtd/NCBI_Mim.mod.dtd b/dtd/NCBI_Mim.mod.dtd new file mode 100644 index 0000000..664a851 --- /dev/null +++ b/dtd/NCBI_Mim.mod.dtd @@ -0,0 +1,354 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + diff --git a/dtd/NCBI_Mime.dtd b/dtd/NCBI_Mime.dtd new file mode 100644 index 0000000..a7be929 --- /dev/null +++ b/dtd/NCBI_Mime.dtd @@ -0,0 +1,113 @@ + + + + + +%NCBI_Entity_module; + + +%EMBL_General_module; + + +%GenBank_General_module; + + +%MMDB_module; + + +%MMDB_Chemical_graph_module; + + +%MMDB_Features_module; + + +%MMDB_Structural_model_module; + + +%NCBI_Biblio_module; + + +%NCBI_BioSource_module; + + +%NCBI_Cdd_module; + + +%NCBI_Cn3d_module; + + +%NCBI_Gene_module; + + +%NCBI_General_module; + + +%NCBI_Medline_module; + + +%NCBI_Mime_module; + + +%NCBI_Organism_module; + + +%NCBI_Protein_module; + + +%NCBI_Pub_module; + + +%NCBI_RNA_module; + + +%NCBI_Rsite_module; + + +%NCBI_ScoreMat_module; + + +%NCBI_SeqTable_module; + + +%NCBI_Seqalign_module; + + +%NCBI_Seqfeat_module; + + +%NCBI_Seqloc_module; + + +%NCBI_Seqres_module; + + +%NCBI_Seqset_module; + + +%NCBI_Sequence_module; + + +%NCBI_TxInit_module; + + +%NCBI_Variation_module; + + +%PDB_General_module; + + +%PIR_General_module; + + +%PRF_General_module; + + +%SP_General_module; diff --git a/dtd/NCBI_Mime.mod.dtd b/dtd/NCBI_Mime.mod.dtd new file mode 100644 index 0000000..a7f8ef4 --- /dev/null +++ b/dtd/NCBI_Mime.mod.dtd @@ -0,0 +1,251 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + diff --git a/dtd/NCBI_ObjPrt.dtd b/dtd/NCBI_ObjPrt.dtd new file mode 100644 index 0000000..ae5196a --- /dev/null +++ b/dtd/NCBI_ObjPrt.dtd @@ -0,0 +1,17 @@ + + + + + +%NCBI_Entity_module; + + +%NCBI_ObjPrt_module; diff --git a/dtd/NCBI_ObjPrt.mod.dtd b/dtd/NCBI_ObjPrt.mod.dtd new file mode 100644 index 0000000..23f916a --- /dev/null +++ b/dtd/NCBI_ObjPrt.mod.dtd @@ -0,0 +1,133 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + diff --git a/dtd/NCBI_Organism.dtd b/dtd/NCBI_Organism.dtd new file mode 100644 index 0000000..b06e17e --- /dev/null +++ b/dtd/NCBI_Organism.dtd @@ -0,0 +1,20 @@ + + + + + +%NCBI_Entity_module; + + +%NCBI_General_module; + + +%NCBI_Organism_module; diff --git a/dtd/NCBI_Organism.mod.dtd b/dtd/NCBI_Organism.mod.dtd new file mode 100644 index 0000000..9c36c43 --- /dev/null +++ b/dtd/NCBI_Organism.mod.dtd @@ -0,0 +1,226 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + diff --git a/dtd/NCBI_PCAssay.dtd b/dtd/NCBI_PCAssay.dtd new file mode 100644 index 0000000..7b35bb2 --- /dev/null +++ b/dtd/NCBI_PCAssay.dtd @@ -0,0 +1,38 @@ + + + + + +%NCBI_Entity_module; + + +%NCBI_Biblio_module; + + +%NCBI_BioSource_module; + + +%NCBI_General_module; + + +%NCBI_Medline_module; + + +%NCBI_Organism_module; + + +%NCBI_PCAssay_module; + + +%NCBI_PCSubstance_module; + + +%NCBI_Pub_module; diff --git a/dtd/NCBI_PCAssay.mod.dtd b/dtd/NCBI_PCAssay.mod.dtd new file mode 100644 index 0000000..020ab07 --- /dev/null +++ b/dtd/NCBI_PCAssay.mod.dtd @@ -0,0 +1,1006 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + diff --git a/dtd/NCBI_PCSubstance.dtd b/dtd/NCBI_PCSubstance.dtd new file mode 100644 index 0000000..0efe6fd --- /dev/null +++ b/dtd/NCBI_PCSubstance.dtd @@ -0,0 +1,29 @@ + + + + + +%NCBI_Entity_module; + + +%NCBI_Biblio_module; + + +%NCBI_General_module; + + +%NCBI_Medline_module; + + +%NCBI_PCSubstance_module; + + +%NCBI_Pub_module; diff --git a/dtd/NCBI_PCSubstance.mod.dtd b/dtd/NCBI_PCSubstance.mod.dtd new file mode 100644 index 0000000..479ed86 --- /dev/null +++ b/dtd/NCBI_PCSubstance.mod.dtd @@ -0,0 +1,1628 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + diff --git a/dtd/NCBI_Project.dtd b/dtd/NCBI_Project.dtd new file mode 100644 index 0000000..4d42013 --- /dev/null +++ b/dtd/NCBI_Project.dtd @@ -0,0 +1,95 @@ + + + + + +%NCBI_Entity_module; + + +%EMBL_General_module; + + +%GenBank_General_module; + + +%NCBI_Biblio_module; + + +%NCBI_BioSource_module; + + +%NCBI_Gene_module; + + +%NCBI_General_module; + + +%NCBI_Medline_module; + + +%NCBI_Organism_module; + + +%NCBI_Project_module; + + +%NCBI_Protein_module; + + +%NCBI_Pub_module; + + +%NCBI_PubMed_module; + + +%NCBI_RNA_module; + + +%NCBI_Rsite_module; + + +%NCBI_SeqTable_module; + + +%NCBI_Seqalign_module; + + +%NCBI_Seqfeat_module; + + +%NCBI_Seqloc_module; + + +%NCBI_Seqres_module; + + +%NCBI_Seqset_module; + + +%NCBI_Sequence_module; + + +%NCBI_TxInit_module; + + +%NCBI_Variation_module; + + +%PDB_General_module; + + +%PIR_General_module; + + +%PRF_General_module; + + +%SP_General_module; diff --git a/dtd/NCBI_Project.mod.dtd b/dtd/NCBI_Project.mod.dtd new file mode 100644 index 0000000..e2215fe --- /dev/null +++ b/dtd/NCBI_Project.mod.dtd @@ -0,0 +1,158 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + diff --git a/dtd/NCBI_Protein.dtd b/dtd/NCBI_Protein.dtd new file mode 100644 index 0000000..e8279ea --- /dev/null +++ b/dtd/NCBI_Protein.dtd @@ -0,0 +1,20 @@ + + + + + +%NCBI_Entity_module; + + +%NCBI_General_module; + + +%NCBI_Protein_module; diff --git a/dtd/NCBI_Protein.mod.dtd b/dtd/NCBI_Protein.mod.dtd new file mode 100644 index 0000000..e833a5d --- /dev/null +++ b/dtd/NCBI_Protein.mod.dtd @@ -0,0 +1,75 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + diff --git a/dtd/NCBI_Pub.dtd b/dtd/NCBI_Pub.dtd new file mode 100644 index 0000000..6a52954 --- /dev/null +++ b/dtd/NCBI_Pub.dtd @@ -0,0 +1,26 @@ + + + + + +%NCBI_Entity_module; + + +%NCBI_Biblio_module; + + +%NCBI_General_module; + + +%NCBI_Medline_module; + + +%NCBI_Pub_module; diff --git a/dtd/NCBI_Pub.mod.dtd b/dtd/NCBI_Pub.mod.dtd new file mode 100644 index 0000000..ca92c18 --- /dev/null +++ b/dtd/NCBI_Pub.mod.dtd @@ -0,0 +1,120 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + diff --git a/dtd/NCBI_PubMed.dtd b/dtd/NCBI_PubMed.dtd new file mode 100644 index 0000000..b272da6 --- /dev/null +++ b/dtd/NCBI_PubMed.dtd @@ -0,0 +1,26 @@ + + + + + +%NCBI_Entity_module; + + +%NCBI_Biblio_module; + + +%NCBI_General_module; + + +%NCBI_Medline_module; + + +%NCBI_PubMed_module; diff --git a/dtd/NCBI_PubMed.mod.dtd b/dtd/NCBI_PubMed.mod.dtd new file mode 100644 index 0000000..4313a76 --- /dev/null +++ b/dtd/NCBI_PubMed.mod.dtd @@ -0,0 +1,64 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + diff --git a/dtd/NCBI_RNA.dtd b/dtd/NCBI_RNA.dtd new file mode 100644 index 0000000..c64fad9 --- /dev/null +++ b/dtd/NCBI_RNA.dtd @@ -0,0 +1,86 @@ + + + + + +%NCBI_Entity_module; + + +%EMBL_General_module; + + +%GenBank_General_module; + + +%NCBI_Biblio_module; + + +%NCBI_BioSource_module; + + +%NCBI_Gene_module; + + +%NCBI_General_module; + + +%NCBI_Medline_module; + + +%NCBI_Organism_module; + + +%NCBI_Protein_module; + + +%NCBI_Pub_module; + + +%NCBI_RNA_module; + + +%NCBI_Rsite_module; + + +%NCBI_SeqTable_module; + + +%NCBI_Seqalign_module; + + +%NCBI_Seqfeat_module; + + +%NCBI_Seqloc_module; + + +%NCBI_Seqres_module; + + +%NCBI_Sequence_module; + + +%NCBI_TxInit_module; + + +%NCBI_Variation_module; + + +%PDB_General_module; + + +%PIR_General_module; + + +%PRF_General_module; + + +%SP_General_module; diff --git a/dtd/NCBI_RNA.mod.dtd b/dtd/NCBI_RNA.mod.dtd new file mode 100644 index 0000000..b1c7991 --- /dev/null +++ b/dtd/NCBI_RNA.mod.dtd @@ -0,0 +1,144 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + diff --git a/dtd/NCBI_Remap.dtd b/dtd/NCBI_Remap.dtd new file mode 100644 index 0000000..4696a50 --- /dev/null +++ b/dtd/NCBI_Remap.dtd @@ -0,0 +1,89 @@ + + + + + +%NCBI_Entity_module; + + +%EMBL_General_module; + + +%GenBank_General_module; + + +%NCBI_Biblio_module; + + +%NCBI_BioSource_module; + + +%NCBI_Gene_module; + + +%NCBI_General_module; + + +%NCBI_Medline_module; + + +%NCBI_Organism_module; + + +%NCBI_Protein_module; + + +%NCBI_Pub_module; + + +%NCBI_RNA_module; + + +%NCBI_Remap_module; + + +%NCBI_Rsite_module; + + +%NCBI_SeqTable_module; + + +%NCBI_Seqalign_module; + + +%NCBI_Seqfeat_module; + + +%NCBI_Seqloc_module; + + +%NCBI_Seqres_module; + + +%NCBI_Sequence_module; + + +%NCBI_TxInit_module; + + +%NCBI_Variation_module; + + +%PDB_General_module; + + +%PIR_General_module; + + +%PRF_General_module; + + +%SP_General_module; diff --git a/dtd/NCBI_Remap.mod.dtd b/dtd/NCBI_Remap.mod.dtd new file mode 100644 index 0000000..9f14d35 --- /dev/null +++ b/dtd/NCBI_Remap.mod.dtd @@ -0,0 +1,158 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + diff --git a/dtd/NCBI_Rsite.dtd b/dtd/NCBI_Rsite.dtd new file mode 100644 index 0000000..7bcf4de --- /dev/null +++ b/dtd/NCBI_Rsite.dtd @@ -0,0 +1,20 @@ + + + + + +%NCBI_Entity_module; + + +%NCBI_General_module; + + +%NCBI_Rsite_module; diff --git a/dtd/NCBI_Rsite.mod.dtd b/dtd/NCBI_Rsite.mod.dtd new file mode 100644 index 0000000..1758ab1 --- /dev/null +++ b/dtd/NCBI_Rsite.mod.dtd @@ -0,0 +1,38 @@ + + + + + + + + + + + + + + + + + + + + + diff --git a/dtd/NCBI_ScoreMat.dtd b/dtd/NCBI_ScoreMat.dtd new file mode 100644 index 0000000..64a676b --- /dev/null +++ b/dtd/NCBI_ScoreMat.dtd @@ -0,0 +1,92 @@ + + + + + +%NCBI_Entity_module; + + +%EMBL_General_module; + + +%GenBank_General_module; + + +%NCBI_Biblio_module; + + +%NCBI_BioSource_module; + + +%NCBI_Gene_module; + + +%NCBI_General_module; + + +%NCBI_Medline_module; + + +%NCBI_Organism_module; + + +%NCBI_Protein_module; + + +%NCBI_Pub_module; + + +%NCBI_RNA_module; + + +%NCBI_Rsite_module; + + +%NCBI_ScoreMat_module; + + +%NCBI_SeqTable_module; + + +%NCBI_Seqalign_module; + + +%NCBI_Seqfeat_module; + + +%NCBI_Seqloc_module; + + +%NCBI_Seqres_module; + + +%NCBI_Seqset_module; + + +%NCBI_Sequence_module; + + +%NCBI_TxInit_module; + + +%NCBI_Variation_module; + + +%PDB_General_module; + + +%PIR_General_module; + + +%PRF_General_module; + + +%SP_General_module; diff --git a/dtd/NCBI_ScoreMat.mod.dtd b/dtd/NCBI_ScoreMat.mod.dtd new file mode 100644 index 0000000..d79b8e0 --- /dev/null +++ b/dtd/NCBI_ScoreMat.mod.dtd @@ -0,0 +1,579 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + diff --git a/dtd/NCBI_SeqCode.dtd b/dtd/NCBI_SeqCode.dtd new file mode 100644 index 0000000..3e754ac --- /dev/null +++ b/dtd/NCBI_SeqCode.dtd @@ -0,0 +1,17 @@ + + + + + +%NCBI_Entity_module; + + +%NCBI_SeqCode_module; diff --git a/dtd/NCBI_SeqCode.mod.dtd b/dtd/NCBI_SeqCode.mod.dtd new file mode 100644 index 0000000..1e60966 --- /dev/null +++ b/dtd/NCBI_SeqCode.mod.dtd @@ -0,0 +1,150 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + diff --git a/dtd/NCBI_SeqTable.dtd b/dtd/NCBI_SeqTable.dtd new file mode 100644 index 0000000..f47d9ba --- /dev/null +++ b/dtd/NCBI_SeqTable.dtd @@ -0,0 +1,86 @@ + + + + + +%NCBI_Entity_module; + + +%EMBL_General_module; + + +%GenBank_General_module; + + +%NCBI_Biblio_module; + + +%NCBI_BioSource_module; + + +%NCBI_Gene_module; + + +%NCBI_General_module; + + +%NCBI_Medline_module; + + +%NCBI_Organism_module; + + +%NCBI_Protein_module; + + +%NCBI_Pub_module; + + +%NCBI_RNA_module; + + +%NCBI_Rsite_module; + + +%NCBI_SeqTable_module; + + +%NCBI_Seqalign_module; + + +%NCBI_Seqfeat_module; + + +%NCBI_Seqloc_module; + + +%NCBI_Seqres_module; + + +%NCBI_Sequence_module; + + +%NCBI_TxInit_module; + + +%NCBI_Variation_module; + + +%PDB_General_module; + + +%PIR_General_module; + + +%PRF_General_module; + + +%SP_General_module; diff --git a/dtd/NCBI_SeqTable.mod.dtd b/dtd/NCBI_SeqTable.mod.dtd new file mode 100644 index 0000000..54232b3 --- /dev/null +++ b/dtd/NCBI_SeqTable.mod.dtd @@ -0,0 +1,390 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + diff --git a/dtd/NCBI_Seq_split.dtd b/dtd/NCBI_Seq_split.dtd new file mode 100644 index 0000000..d705b7c --- /dev/null +++ b/dtd/NCBI_Seq_split.dtd @@ -0,0 +1,92 @@ + + + + + +%NCBI_Entity_module; + + +%EMBL_General_module; + + +%GenBank_General_module; + + +%NCBI_Biblio_module; + + +%NCBI_BioSource_module; + + +%NCBI_Gene_module; + + +%NCBI_General_module; + + +%NCBI_Medline_module; + + +%NCBI_Organism_module; + + +%NCBI_Protein_module; + + +%NCBI_Pub_module; + + +%NCBI_RNA_module; + + +%NCBI_Rsite_module; + + +%NCBI_Seq_split_module; + + +%NCBI_SeqTable_module; + + +%NCBI_Seqalign_module; + + +%NCBI_Seqfeat_module; + + +%NCBI_Seqloc_module; + + +%NCBI_Seqres_module; + + +%NCBI_Seqset_module; + + +%NCBI_Sequence_module; + + +%NCBI_TxInit_module; + + +%NCBI_Variation_module; + + +%PDB_General_module; + + +%PIR_General_module; + + +%PRF_General_module; + + +%SP_General_module; diff --git a/dtd/NCBI_Seq_split.mod.dtd b/dtd/NCBI_Seq_split.mod.dtd new file mode 100644 index 0000000..4ab94ad --- /dev/null +++ b/dtd/NCBI_Seq_split.mod.dtd @@ -0,0 +1,559 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + diff --git a/dtd/NCBI_Seqalign.dtd b/dtd/NCBI_Seqalign.dtd new file mode 100644 index 0000000..08e37eb --- /dev/null +++ b/dtd/NCBI_Seqalign.dtd @@ -0,0 +1,86 @@ + + + + + +%NCBI_Entity_module; + + +%EMBL_General_module; + + +%GenBank_General_module; + + +%NCBI_Biblio_module; + + +%NCBI_BioSource_module; + + +%NCBI_Gene_module; + + +%NCBI_General_module; + + +%NCBI_Medline_module; + + +%NCBI_Organism_module; + + +%NCBI_Protein_module; + + +%NCBI_Pub_module; + + +%NCBI_RNA_module; + + +%NCBI_Rsite_module; + + +%NCBI_SeqTable_module; + + +%NCBI_Seqalign_module; + + +%NCBI_Seqfeat_module; + + +%NCBI_Seqloc_module; + + +%NCBI_Seqres_module; + + +%NCBI_Sequence_module; + + +%NCBI_TxInit_module; + + +%NCBI_Variation_module; + + +%PDB_General_module; + + +%PIR_General_module; + + +%PRF_General_module; + + +%SP_General_module; diff --git a/dtd/NCBI_Seqalign.mod.dtd b/dtd/NCBI_Seqalign.mod.dtd new file mode 100644 index 0000000..721a351 --- /dev/null +++ b/dtd/NCBI_Seqalign.mod.dtd @@ -0,0 +1,570 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + diff --git a/dtd/NCBI_Seqfeat.dtd b/dtd/NCBI_Seqfeat.dtd new file mode 100644 index 0000000..48af83f --- /dev/null +++ b/dtd/NCBI_Seqfeat.dtd @@ -0,0 +1,86 @@ + + + + + +%NCBI_Entity_module; + + +%EMBL_General_module; + + +%GenBank_General_module; + + +%NCBI_Biblio_module; + + +%NCBI_BioSource_module; + + +%NCBI_Gene_module; + + +%NCBI_General_module; + + +%NCBI_Medline_module; + + +%NCBI_Organism_module; + + +%NCBI_Protein_module; + + +%NCBI_Pub_module; + + +%NCBI_RNA_module; + + +%NCBI_Rsite_module; + + +%NCBI_SeqTable_module; + + +%NCBI_Seqalign_module; + + +%NCBI_Seqfeat_module; + + +%NCBI_Seqloc_module; + + +%NCBI_Seqres_module; + + +%NCBI_Sequence_module; + + +%NCBI_TxInit_module; + + +%NCBI_Variation_module; + + +%PDB_General_module; + + +%PIR_General_module; + + +%PRF_General_module; + + +%SP_General_module; diff --git a/dtd/NCBI_Seqfeat.mod.dtd b/dtd/NCBI_Seqfeat.mod.dtd new file mode 100644 index 0000000..fb7dc75 --- /dev/null +++ b/dtd/NCBI_Seqfeat.mod.dtd @@ -0,0 +1,772 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + diff --git a/dtd/NCBI_Seqloc.dtd b/dtd/NCBI_Seqloc.dtd new file mode 100644 index 0000000..a0464a4 --- /dev/null +++ b/dtd/NCBI_Seqloc.dtd @@ -0,0 +1,86 @@ + + + + + +%NCBI_Entity_module; + + +%EMBL_General_module; + + +%GenBank_General_module; + + +%NCBI_Biblio_module; + + +%NCBI_BioSource_module; + + +%NCBI_Gene_module; + + +%NCBI_General_module; + + +%NCBI_Medline_module; + + +%NCBI_Organism_module; + + +%NCBI_Protein_module; + + +%NCBI_Pub_module; + + +%NCBI_RNA_module; + + +%NCBI_Rsite_module; + + +%NCBI_SeqTable_module; + + +%NCBI_Seqalign_module; + + +%NCBI_Seqfeat_module; + + +%NCBI_Seqloc_module; + + +%NCBI_Seqres_module; + + +%NCBI_Sequence_module; + + +%NCBI_TxInit_module; + + +%NCBI_Variation_module; + + +%PDB_General_module; + + +%PIR_General_module; + + +%PRF_General_module; + + +%SP_General_module; diff --git a/dtd/NCBI_Seqloc.mod.dtd b/dtd/NCBI_Seqloc.mod.dtd new file mode 100644 index 0000000..7daa894 --- /dev/null +++ b/dtd/NCBI_Seqloc.mod.dtd @@ -0,0 +1,325 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + diff --git a/dtd/NCBI_Seqres.dtd b/dtd/NCBI_Seqres.dtd new file mode 100644 index 0000000..353ff75 --- /dev/null +++ b/dtd/NCBI_Seqres.dtd @@ -0,0 +1,86 @@ + + + + + +%NCBI_Entity_module; + + +%EMBL_General_module; + + +%GenBank_General_module; + + +%NCBI_Biblio_module; + + +%NCBI_BioSource_module; + + +%NCBI_Gene_module; + + +%NCBI_General_module; + + +%NCBI_Medline_module; + + +%NCBI_Organism_module; + + +%NCBI_Protein_module; + + +%NCBI_Pub_module; + + +%NCBI_RNA_module; + + +%NCBI_Rsite_module; + + +%NCBI_SeqTable_module; + + +%NCBI_Seqalign_module; + + +%NCBI_Seqfeat_module; + + +%NCBI_Seqloc_module; + + +%NCBI_Seqres_module; + + +%NCBI_Sequence_module; + + +%NCBI_TxInit_module; + + +%NCBI_Variation_module; + + +%PDB_General_module; + + +%PIR_General_module; + + +%PRF_General_module; + + +%SP_General_module; diff --git a/dtd/NCBI_Seqres.mod.dtd b/dtd/NCBI_Seqres.mod.dtd new file mode 100644 index 0000000..27dba62 --- /dev/null +++ b/dtd/NCBI_Seqres.mod.dtd @@ -0,0 +1,134 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + diff --git a/dtd/NCBI_Seqset.dtd b/dtd/NCBI_Seqset.dtd new file mode 100644 index 0000000..69de4db --- /dev/null +++ b/dtd/NCBI_Seqset.dtd @@ -0,0 +1,89 @@ + + + + + +%NCBI_Entity_module; + + +%EMBL_General_module; + + +%GenBank_General_module; + + +%NCBI_Biblio_module; + + +%NCBI_BioSource_module; + + +%NCBI_Gene_module; + + +%NCBI_General_module; + + +%NCBI_Medline_module; + + +%NCBI_Organism_module; + + +%NCBI_Protein_module; + + +%NCBI_Pub_module; + + +%NCBI_RNA_module; + + +%NCBI_Rsite_module; + + +%NCBI_SeqTable_module; + + +%NCBI_Seqalign_module; + + +%NCBI_Seqfeat_module; + + +%NCBI_Seqloc_module; + + +%NCBI_Seqres_module; + + +%NCBI_Seqset_module; + + +%NCBI_Sequence_module; + + +%NCBI_TxInit_module; + + +%NCBI_Variation_module; + + +%PDB_General_module; + + +%PIR_General_module; + + +%PRF_General_module; + + +%SP_General_module; diff --git a/dtd/NCBI_Seqset.mod.dtd b/dtd/NCBI_Seqset.mod.dtd new file mode 100644 index 0000000..549d8d6 --- /dev/null +++ b/dtd/NCBI_Seqset.mod.dtd @@ -0,0 +1,138 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + diff --git a/dtd/NCBI_Sequence.dtd b/dtd/NCBI_Sequence.dtd new file mode 100644 index 0000000..78673f6 --- /dev/null +++ b/dtd/NCBI_Sequence.dtd @@ -0,0 +1,86 @@ + + + + + +%NCBI_Entity_module; + + +%EMBL_General_module; + + +%GenBank_General_module; + + +%NCBI_Biblio_module; + + +%NCBI_BioSource_module; + + +%NCBI_Gene_module; + + +%NCBI_General_module; + + +%NCBI_Medline_module; + + +%NCBI_Organism_module; + + +%NCBI_Protein_module; + + +%NCBI_Pub_module; + + +%NCBI_RNA_module; + + +%NCBI_Rsite_module; + + +%NCBI_SeqTable_module; + + +%NCBI_Seqalign_module; + + +%NCBI_Seqfeat_module; + + +%NCBI_Seqloc_module; + + +%NCBI_Seqres_module; + + +%NCBI_Sequence_module; + + +%NCBI_TxInit_module; + + +%NCBI_Variation_module; + + +%PDB_General_module; + + +%PIR_General_module; + + +%PRF_General_module; + + +%SP_General_module; diff --git a/dtd/NCBI_Sequence.mod.dtd b/dtd/NCBI_Sequence.mod.dtd new file mode 100644 index 0000000..d09ae02 --- /dev/null +++ b/dtd/NCBI_Sequence.mod.dtd @@ -0,0 +1,1112 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + diff --git a/dtd/NCBI_Submit.dtd b/dtd/NCBI_Submit.dtd new file mode 100644 index 0000000..b81b188 --- /dev/null +++ b/dtd/NCBI_Submit.dtd @@ -0,0 +1,92 @@ + + + + + +%NCBI_Entity_module; + + +%EMBL_General_module; + + +%GenBank_General_module; + + +%NCBI_Biblio_module; + + +%NCBI_BioSource_module; + + +%NCBI_Gene_module; + + +%NCBI_General_module; + + +%NCBI_Medline_module; + + +%NCBI_Organism_module; + + +%NCBI_Protein_module; + + +%NCBI_Pub_module; + + +%NCBI_RNA_module; + + +%NCBI_Rsite_module; + + +%NCBI_SeqTable_module; + + +%NCBI_Seqalign_module; + + +%NCBI_Seqfeat_module; + + +%NCBI_Seqloc_module; + + +%NCBI_Seqres_module; + + +%NCBI_Seqset_module; + + +%NCBI_Sequence_module; + + +%NCBI_Submit_module; + + +%NCBI_TxInit_module; + + +%NCBI_Variation_module; + + +%PDB_General_module; + + +%PIR_General_module; + + +%PRF_General_module; + + +%SP_General_module; diff --git a/dtd/NCBI_Submit.mod.dtd b/dtd/NCBI_Submit.mod.dtd new file mode 100644 index 0000000..64885f0 --- /dev/null +++ b/dtd/NCBI_Submit.mod.dtd @@ -0,0 +1,156 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + diff --git a/dtd/NCBI_Systems.dtd b/dtd/NCBI_Systems.dtd new file mode 100644 index 0000000..d1f8c2a --- /dev/null +++ b/dtd/NCBI_Systems.dtd @@ -0,0 +1,86 @@ + + + + + +%NCBI_Entity_module; + + +%EMBL_General_module; + + +%GenBank_General_module; + + +%NCBI_Biblio_module; + + +%NCBI_BioSource_module; + + +%NCBI_Gene_module; + + +%NCBI_General_module; + + +%NCBI_Medline_module; + + +%NCBI_Organism_module; + + +%NCBI_Protein_module; + + +%NCBI_Pub_module; + + +%NCBI_RNA_module; + + +%NCBI_Rsite_module; + + +%NCBI_SeqTable_module; + + +%NCBI_Seqalign_module; + + +%NCBI_Seqfeat_module; + + +%NCBI_Seqloc_module; + + +%NCBI_Seqres_module; + + +%NCBI_Sequence_module; + + +%NCBI_Systems_module; + + +%NCBI_TxInit_module; + + +%PDB_General_module; + + +%PIR_General_module; + + +%PRF_General_module; + + +%SP_General_module; diff --git a/dtd/NCBI_TSeq.dtd b/dtd/NCBI_TSeq.dtd new file mode 100644 index 0000000..9463557 --- /dev/null +++ b/dtd/NCBI_TSeq.dtd @@ -0,0 +1,17 @@ + + + + + +%NCBI_Entity_module; + + +%NCBI_TSeq_module; diff --git a/dtd/NCBI_TSeq.mod.dtd b/dtd/NCBI_TSeq.mod.dtd new file mode 100644 index 0000000..e7fc3f4 --- /dev/null +++ b/dtd/NCBI_TSeq.mod.dtd @@ -0,0 +1,66 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + diff --git a/dtd/NCBI_TxInit.dtd b/dtd/NCBI_TxInit.dtd new file mode 100644 index 0000000..fe9a6c1 --- /dev/null +++ b/dtd/NCBI_TxInit.dtd @@ -0,0 +1,29 @@ + + + + + +%NCBI_Entity_module; + + +%NCBI_Gene_module; + + +%NCBI_General_module; + + +%NCBI_Organism_module; + + +%NCBI_Protein_module; + + +%NCBI_TxInit_module; diff --git a/dtd/NCBI_TxInit.mod.dtd b/dtd/NCBI_TxInit.mod.dtd new file mode 100644 index 0000000..d5d97c1 --- /dev/null +++ b/dtd/NCBI_TxInit.mod.dtd @@ -0,0 +1,184 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + diff --git a/dtd/NCBI_Variation.dtd b/dtd/NCBI_Variation.dtd new file mode 100644 index 0000000..7a992b1 --- /dev/null +++ b/dtd/NCBI_Variation.dtd @@ -0,0 +1,86 @@ + + + + + +%NCBI_Entity_module; + + +%EMBL_General_module; + + +%GenBank_General_module; + + +%NCBI_Biblio_module; + + +%NCBI_BioSource_module; + + +%NCBI_Gene_module; + + +%NCBI_General_module; + + +%NCBI_Medline_module; + + +%NCBI_Organism_module; + + +%NCBI_Protein_module; + + +%NCBI_Pub_module; + + +%NCBI_RNA_module; + + +%NCBI_Rsite_module; + + +%NCBI_SeqTable_module; + + +%NCBI_Seqalign_module; + + +%NCBI_Seqfeat_module; + + +%NCBI_Seqloc_module; + + +%NCBI_Seqres_module; + + +%NCBI_Sequence_module; + + +%NCBI_TxInit_module; + + +%NCBI_Variation_module; + + +%PDB_General_module; + + +%PIR_General_module; + + +%PRF_General_module; + + +%SP_General_module; diff --git a/dtd/NCBI_Variation.mod.dtd b/dtd/NCBI_Variation.mod.dtd new file mode 100644 index 0000000..ee7f020 --- /dev/null +++ b/dtd/NCBI_Variation.mod.dtd @@ -0,0 +1,944 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + diff --git a/dtd/NCBI_all.dtd b/dtd/NCBI_all.dtd new file mode 100644 index 0000000..3ed101d --- /dev/null +++ b/dtd/NCBI_all.dtd @@ -0,0 +1,202 @@ + + +%NCBI_Entity_module; + + +%Docsum_3_0_module; + + +%Docsum_3_1_module; + + +%Docsum_3_2_module; + + +%Docsum_3_3_module; + + +%Docsum_3_4_module; + + +%EMBL_General_module; + + +%GenBank_General_module; + + +%HomoloGene_module; + + +%INSD_INSDSeq_module; + + +%MMDB_module; + + +%MMDB_Chemical_graph_module; + + +%MMDB_Features_module; + + +%MMDB_Structural_model_module; + + +%NCBI_Access_module; + + +%NCBI_Biblio_module; + + +%NCBI_BioSource_module; + + +%NCBI_BioTree_module; + + +%NCBI_Blast4_module; + + +%NCBI_BlastDL_module; + + +%NCBI_BlastOutput_module; + + +%NCBI_Cdd_module; + + +%NCBI_Cn3d_module; + + +%NCBI_Entrez2_module; + + +%NCBI_Entrezgene_module; + + +%NCBI_FeatDef_module; + + +%NCBI_GBSeq_module; + + +%NCBI_Gene_module; + + +%NCBI_General_module; + + +%NCBI_ID1Access_module; + + +%NCBI_ID2Access_module; + + +%NCBI_MedArchive_module; + + +%NCBI_Medlars_module; + + +%NCBI_Medline_module; + + +%NCBI_Mim_module; + + +%NCBI_Mime_module; + + +%NCBI_ObjPrt_module; + + +%NCBI_Organism_module; + + +%NCBI_PCAssay_module; + + +%NCBI_PCSubstance_module; + + +%NCBI_Project_module; + + +%NCBI_Protein_module; + + +%NCBI_Pub_module; + + +%NCBI_PubMed_module; + + +%NCBI_RNA_module; + + +%NCBI_Remap_module; + + +%NCBI_Rsite_module; + + +%NCBI_ScoreMat_module; + + +%NCBI_SeqCode_module; + + +%NCBI_SeqTable_module; + + +%NCBI_Seq_split_module; + + +%NCBI_Seqalign_module; + + +%NCBI_Seqfeat_module; + + +%NCBI_Seqloc_module; + + +%NCBI_Seqres_module; + + +%NCBI_Seqset_module; + + +%NCBI_Sequence_module; + + +%NCBI_Submit_module; + + +%NCBI_TSeq_module; + + +%NCBI_TxInit_module; + + +%NCBI_Variation_module; + + +%NSE_module; + + +%OMSSA_module; + + +%PDB_General_module; + + +%PIR_General_module; + + +%PRF_General_module; + + +%SP_General_module; + diff --git a/dtd/NSE.dtd b/dtd/NSE.dtd new file mode 100644 index 0000000..74f0075 --- /dev/null +++ b/dtd/NSE.dtd @@ -0,0 +1,17 @@ + + + + + +%NCBI_Entity_module; + + +%NSE_module; diff --git a/dtd/NSE.mod.dtd b/dtd/NSE.mod.dtd new file mode 100644 index 0000000..4327f48 --- /dev/null +++ b/dtd/NSE.mod.dtd @@ -0,0 +1,895 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + 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/dev/null +++ b/dtd/nlmmedline_090101.dtd @@ -0,0 +1,74 @@ + + + + + + + + + + + + + + + + + + + + + + +%MedlineCitation; + + + + diff --git a/dtd/nlmmedlinecitation_011101.dtd b/dtd/nlmmedlinecitation_011101.dtd new file mode 100644 index 0000000..6b8a447 --- /dev/null +++ b/dtd/nlmmedlinecitation_011101.dtd @@ -0,0 +1,178 @@ + + + + + + + + + + +%NlmCommon; + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + diff --git a/dtd/nlmmedlinecitation_060101.dtd b/dtd/nlmmedlinecitation_060101.dtd new file mode 100644 index 0000000..03ff193 --- /dev/null +++ b/dtd/nlmmedlinecitation_060101.dtd @@ -0,0 +1,103 @@ + + + + + + + + + + + + + + + +%NlmSharedCatCit; + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + diff --git a/dtd/nlmmedlinecitation_070101.dtd b/dtd/nlmmedlinecitation_070101.dtd new file mode 100644 index 0000000..35fc73d --- /dev/null +++ b/dtd/nlmmedlinecitation_070101.dtd @@ -0,0 +1,104 @@ + + + + + + + + + + + + + + + +%NlmSharedCatCit; + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + diff --git a/dtd/nlmmedlinecitation_080101.dtd b/dtd/nlmmedlinecitation_080101.dtd new file mode 100644 index 0000000..670005a --- /dev/null +++ b/dtd/nlmmedlinecitation_080101.dtd @@ -0,0 +1,107 @@ + + + + + + + + + + + + + + + + + + +%NlmSharedCatCit; + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + diff --git a/dtd/nlmmedlinecitation_090101.dtd b/dtd/nlmmedlinecitation_090101.dtd new file mode 100644 index 0000000..1987031 --- /dev/null +++ b/dtd/nlmmedlinecitation_090101.dtd @@ -0,0 +1,112 @@ + + + + + + + + + + + + + + + + + +%NlmSharedCatCit; + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + diff --git a/dtd/nlmmedlinecitationset_100101.dtd b/dtd/nlmmedlinecitationset_100101.dtd new file mode 100644 index 0000000..16fc7fa --- /dev/null +++ b/dtd/nlmmedlinecitationset_100101.dtd @@ -0,0 +1,194 @@ + + + + + + + + + + + + + + + + + + + + + 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+ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + diff --git a/dtd/nlmmedlinecitationset_120101.dtd b/dtd/nlmmedlinecitationset_120101.dtd new file mode 100644 index 0000000..6489a8c --- /dev/null +++ b/dtd/nlmmedlinecitationset_120101.dtd @@ -0,0 +1,188 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + diff --git a/dtd/nlmmedlinecitationset_130101.dtd b/dtd/nlmmedlinecitationset_130101.dtd new file mode 100644 index 0000000..cda3746 --- /dev/null +++ b/dtd/nlmmedlinecitationset_130101.dtd @@ -0,0 +1,191 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + diff --git a/dtd/nlmmedlinecitationset_130501.dtd b/dtd/nlmmedlinecitationset_130501.dtd new file mode 100644 index 0000000..9566d38 --- /dev/null +++ b/dtd/nlmmedlinecitationset_130501.dtd @@ -0,0 +1,191 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + diff --git a/dtd/nlmmedlinecitationset_140101.dtd b/dtd/nlmmedlinecitationset_140101.dtd new file mode 100644 index 0000000..d8238d9 --- /dev/null +++ b/dtd/nlmmedlinecitationset_140101.dtd @@ -0,0 +1,190 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + diff --git a/dtd/nlmmedlinecitationset_150101.dtd b/dtd/nlmmedlinecitationset_150101.dtd new file mode 100644 index 0000000..2d90743 --- /dev/null +++ b/dtd/nlmmedlinecitationset_150101.dtd @@ -0,0 +1,189 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + diff --git a/dtd/nlmmedlinecitationset_160101.dtd b/dtd/nlmmedlinecitationset_160101.dtd new file mode 100644 index 0000000..0be6562 --- /dev/null +++ b/dtd/nlmmedlinecitationset_160101.dtd @@ -0,0 +1,180 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + diff --git a/dtd/nlmserials_080101.dtd b/dtd/nlmserials_080101.dtd new file mode 100644 index 0000000..c5781d8 --- /dev/null +++ b/dtd/nlmserials_080101.dtd @@ -0,0 +1,134 @@ + + + + + + + + + + + + + + + + + + + + + +%NlmCommon; + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + diff --git a/dtd/nlmserials_100101.dtd b/dtd/nlmserials_100101.dtd new file mode 100644 index 0000000..87c1dc2 --- /dev/null +++ b/dtd/nlmserials_100101.dtd @@ -0,0 +1,157 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + diff --git a/dtd/nlmsharedcatcit_060101.dtd b/dtd/nlmsharedcatcit_060101.dtd new file mode 100644 index 0000000..d909d83 --- /dev/null +++ b/dtd/nlmsharedcatcit_060101.dtd @@ -0,0 +1,81 @@ + + + + + + +%NlmCommon; + + + + + + + + + + + + + + + + + + + + + + + + diff --git a/dtd/nlmsharedcatcit_070101.dtd b/dtd/nlmsharedcatcit_070101.dtd new file mode 100644 index 0000000..bf75c3c --- /dev/null +++ b/dtd/nlmsharedcatcit_070101.dtd @@ -0,0 +1,81 @@ + + + + + + + + + + +%NlmCommon; + + + + + + + + + + + + + + + + + + + + + + + diff --git a/dtd/nlmsharedcatcit_080101.dtd b/dtd/nlmsharedcatcit_080101.dtd new file mode 100644 index 0000000..f7397ea --- /dev/null +++ b/dtd/nlmsharedcatcit_080101.dtd @@ -0,0 +1,80 @@ + + + + + + + + + + +%NlmCommon; + + + + + + + + + + + + + + + + + + + + + diff --git a/dtd/nlmsharedcatcit_090101.dtd b/dtd/nlmsharedcatcit_090101.dtd new file mode 100644 index 0000000..2a41d3e --- /dev/null +++ b/dtd/nlmsharedcatcit_090101.dtd @@ -0,0 +1,80 @@ + + + + + + + + + + +%NlmCommon; + + + + + + + + + + + + + + + + + + + diff --git a/dtd/notat.ent b/dtd/notat.ent new file mode 100644 index 0000000..b46a91d --- /dev/null +++ b/dtd/notat.ent @@ -0,0 +1,172 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + diff --git a/dtd/para.ent b/dtd/para.ent new file mode 100644 index 0000000..3c2f114 --- /dev/null +++ b/dtd/para.ent @@ -0,0 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index 0000000..62b71f8 --- /dev/null +++ b/dtd/pubmed_100101.dtd @@ -0,0 +1,72 @@ + + + + + +%Medline; + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + diff --git a/dtd/pubmed_100301.dtd b/dtd/pubmed_100301.dtd new file mode 100644 index 0000000..adc5272 --- /dev/null +++ b/dtd/pubmed_100301.dtd @@ -0,0 +1,79 @@ + + + + + +%Medline; + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +%Bookdoc; + diff --git a/dtd/pubmed_110101.dtd b/dtd/pubmed_110101.dtd new file mode 100644 index 0000000..6298eb6 --- /dev/null +++ b/dtd/pubmed_110101.dtd @@ -0,0 +1,79 @@ + + + + + +%Medline; + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +%Bookdoc; + diff --git a/dtd/pubmed_120101.dtd b/dtd/pubmed_120101.dtd new file mode 100644 index 0000000..dacafb8 --- /dev/null +++ b/dtd/pubmed_120101.dtd @@ -0,0 +1,79 @@ + + + + + +%Medline; + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +%Bookdoc; + diff --git a/dtd/pubmed_130101.dtd b/dtd/pubmed_130101.dtd new file mode 100644 index 0000000..82bd9c6 --- /dev/null +++ b/dtd/pubmed_130101.dtd @@ -0,0 +1,79 @@ + + + + + +%Medline; + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +%Bookdoc; + diff --git a/dtd/pubmed_130501.dtd b/dtd/pubmed_130501.dtd new file mode 100644 index 0000000..a3c640c --- /dev/null +++ b/dtd/pubmed_130501.dtd @@ -0,0 +1,79 @@ + + + + + +%Medline; + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +%Bookdoc; + diff --git a/dtd/pubmed_140101.dtd b/dtd/pubmed_140101.dtd new file mode 100644 index 0000000..4570815 --- /dev/null +++ b/dtd/pubmed_140101.dtd @@ -0,0 +1,79 @@ + + + + + +%Medline; + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +%Bookdoc; + diff --git a/dtd/pubmed_150101.dtd b/dtd/pubmed_150101.dtd new file mode 100644 index 0000000..7c0933d --- /dev/null +++ b/dtd/pubmed_150101.dtd @@ -0,0 +1,79 @@ + + + + + +%Medline; + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +%Bookdoc; + diff --git a/dtd/pubmed_180101.dtd b/dtd/pubmed_180101.dtd new file mode 100644 index 0000000..48bec8a --- /dev/null +++ b/dtd/pubmed_180101.dtd @@ -0,0 +1,434 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + diff --git a/dtd/pubmed_180601.dtd b/dtd/pubmed_180601.dtd new file mode 100644 index 0000000..aab61e7 --- /dev/null +++ b/dtd/pubmed_180601.dtd @@ -0,0 +1,454 @@ + + + + + + + +%mathml-in-pubmed; + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + diff --git a/dtd/pubmed_190101.dtd b/dtd/pubmed_190101.dtd new file mode 100644 index 0000000..a1cd167 --- /dev/null +++ b/dtd/pubmed_190101.dtd @@ -0,0 +1,478 @@ + + + + + + + +%mathml-in-pubmed; + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + diff --git a/dtd/pubmed_230101.dtd b/dtd/pubmed_230101.dtd new file mode 100644 index 0000000..fb1354e --- /dev/null +++ b/dtd/pubmed_230101.dtd @@ -0,0 +1,468 @@ + + + + + + + +%mathml-in-pubmed; + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + diff --git a/dtd/references.ent b/dtd/references.ent new file mode 100644 index 0000000..591cb9f --- /dev/null +++ b/dtd/references.ent @@ -0,0 +1,726 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + diff --git a/dtd/section.ent b/dtd/section.ent new file mode 100644 index 0000000..17d0128 --- /dev/null +++ b/dtd/section.ent @@ -0,0 +1,220 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + diff --git a/dtd/taxon.dtd b/dtd/taxon.dtd new file mode 100644 index 0000000..fadf481 --- /dev/null +++ b/dtd/taxon.dtd @@ -0,0 +1,131 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + diff --git a/dtd/xhtml-inlstyle-1.mod b/dtd/xhtml-inlstyle-1.mod new file mode 100644 index 0000000..79accd4 --- /dev/null +++ b/dtd/xhtml-inlstyle-1.mod @@ -0,0 +1,34 @@ + + + + + + + + + + + + \ No newline at end of file diff --git a/dtd/xhtml-table-1.mod b/dtd/xhtml-table-1.mod new file mode 100644 index 0000000..2b8eeef --- /dev/null +++ b/dtd/xhtml-table-1.mod @@ -0,0 +1,333 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +]]> + + + +]]> + + + + + + +]]> + + + +]]> + + + + + + + + +]]> + + + +]]> + + + + + + + + +]]> + + + +]]> + + + + + + + + +]]> + + + +]]> + + + + + + + + +]]> + + + +]]> + + + + + + + + +]]> + + + +]]> + + + + + + +]]> + + + +]]> + + + + + + + + +]]> + + + +]]> + + + + + + +]]> + + + +]]> + + \ No newline at end of file diff --git a/dtd/xmlspecchars.ent b/dtd/xmlspecchars.ent new file mode 100644 index 0000000..bb15ade --- /dev/null +++ b/dtd/xmlspecchars.ent @@ -0,0 +1,290 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + +%ISOlat1; +%ISOlat2; +%ISObox; +%ISOdia; +%ISOnum; +%ISOpub; +%ISOtech; +%ISOgrk1; +%ISOgrk2; +%ISOgrk3; +%ISOgrk4; +%ISOcyr1; +%ISOcyr2; +%ISOamsa; +%ISOamsb; +%ISOamsc; +%ISOamsn; +%ISOamso; +%ISOamsr; +%ISOmscr; +%ISOmfrk; +%ISOmopf; + + + + + + diff --git a/src/main/java/com/curehunter/transform/TransformAll.java b/src/main/java/com/curehunter/transform/TransformAll.java index 71e996a..6898ae4 100644 --- a/src/main/java/com/curehunter/transform/TransformAll.java +++ b/src/main/java/com/curehunter/transform/TransformAll.java @@ -8,19 +8,25 @@ import java.util.concurrent.TimeUnit; import java.util.zip.GZIPInputStream; +import javax.xml.parsers.SAXParser; import javax.xml.parsers.SAXParserFactory; import javax.xml.transform.Transformer; import javax.xml.transform.TransformerFactory; +import javax.xml.transform.sax.SAXSource; import javax.xml.transform.stream.StreamResult; import javax.xml.transform.stream.StreamSource; import com.curehunter.utils.FileIterator; +import com.curehunter.utils.LocalCacheEntityResolver; import java.nio.file.Path; import java.nio.file.Paths; import java.util.concurrent.Callable; import org.apache.commons.io.filefilter.WildcardFileFilter; +import org.xml.sax.InputSource; +import org.xml.sax.XMLReader; + import picocli.CommandLine.Command; import picocli.CommandLine.Option; @@ -42,6 +48,9 @@ public class TransformAll implements Callable { @Option(names = { "-x", "--xsl" }, description = "XSL file to use for transformation, default: ./xsl/medlineCitationTSV.xsl") private Path xslFile = Paths.get(System.getProperty("user.dir")+"/xsl/medlineCitationTSV.xsl"); + @Option(names = { "-d", "--dtd" }, description = "local copies of DTDs referenced in XML to avoid remote lookup, default: ./dtd") + private Path dtdDir = Paths.get(System.getProperty("user.dir")+"/dtd"); + @Option(names = { "-e", "--outExt" }, description = "extension to append to output files, default: .out", defaultValue = ".out") private String outputExtension; @@ -56,10 +65,14 @@ public Integer call() { try { System.out.println("in=" + inputDir.toFile().getCanonicalPath() + " out=" + outputDir.toFile().getCanonicalPath() - + " xsl=" + xslFile.toFile().getCanonicalPath()); + + " xsl=" + xslFile.toFile().getCanonicalPath() + + " dtd=" + dtdDir.toFile().getCanonicalPath() + + " workers=" + workerThreads + + " filter=" + filterPattern + + " outputExtension=" + outputExtension); ExecutorService exec = Executors.newFixedThreadPool(workerThreads); for (int n = 0; n < workerThreads; n++) { - exec.execute(new Worker(workerData, xslFile.toFile(), outputDir.toFile(), + exec.execute(new Worker(workerData, xslFile.toFile(), dtdDir.toFile(), outputDir.toFile(), outputExtension, filter)); } exec.shutdown(); @@ -78,14 +91,16 @@ public Integer call() { static class Worker implements Runnable { FileIterator workerData; File xslt; + File dtdDir; File outputDir; String outputExtension; WildcardFileFilter filter; - public Worker(FileIterator workerData, File xslt, File outputDir, String outputExtension, + public Worker(FileIterator workerData, File xslt, File dtdDir, File outputDir, String outputExtension, WildcardFileFilter filter) { this.workerData = workerData; this.xslt = xslt; + this.dtdDir = dtdDir; this.outputDir = outputDir; this.outputExtension = outputExtension; this.filter = filter; @@ -96,16 +111,20 @@ public void run() { TransformerFactory transformerFactory = TransformerFactory.newInstance(); System.out.println("transformerFactory=" + transformerFactory + " parserFactory=" + parserFactory); try { + SAXParser saxParser = parserFactory.newSAXParser(); + XMLReader xmlReader = saxParser.getXMLReader(); + xmlReader.setEntityResolver(new LocalCacheEntityResolver(dtdDir)); Transformer transformer = transformerFactory.newTransformer(new StreamSource(xslt)); File f = null; while ((f = workerData.next()) != null) { if (filter.accept(f)) { System.out.println("start transforming file=" + f.getCanonicalPath()); try { - transformer.transform(new StreamSource( - f.getCanonicalPath().toLowerCase().endsWith(".gz") + SAXSource saxSource = new SAXSource(xmlReader, new InputSource( + f.getCanonicalPath().toLowerCase().endsWith(".gz") ? new GZIPInputStream(new FileInputStream(f)) - : new FileInputStream(f)), + : new FileInputStream(f))); + transformer.transform(saxSource, new StreamResult(new File(outputDir, f.getName() + outputExtension))); System.out.println("done transforming file=" + f.getCanonicalPath()); } catch (Throwable e) { diff --git a/src/main/java/com/curehunter/utils/LocalCacheEntityResolver.java b/src/main/java/com/curehunter/utils/LocalCacheEntityResolver.java new file mode 100644 index 0000000..59d4dfd --- /dev/null +++ b/src/main/java/com/curehunter/utils/LocalCacheEntityResolver.java @@ -0,0 +1,34 @@ +package com.curehunter.utils; + +import java.io.File; +import java.io.FileReader; +import java.io.IOException; + +import org.xml.sax.EntityResolver; +import org.xml.sax.InputSource; +import org.xml.sax.SAXException; + +public class LocalCacheEntityResolver implements EntityResolver { + private File dtdDirectory; + + public LocalCacheEntityResolver(File dtdDirectory) { + this.dtdDirectory = dtdDirectory; + } + + public InputSource resolveEntity(String publicId, String systemId) + throws SAXException, IOException { + if (systemId != null && dtdDirectory != null) { + int lastSlash = systemId.lastIndexOf('/'); + String dtdFile = lastSlash != -1 ? systemId.substring(lastSlash + 1) : systemId; + File candidate = new File(dtdDirectory, dtdFile); + if (candidate.exists() && candidate.isFile()) { + InputSource source = new InputSource(new FileReader(candidate)); + source.setSystemId(candidate.getAbsolutePath()); + return source; + } else { + System.err.println("Entity not found in directory, forcing remote lookup: " + systemId + " (public: " + publicId + ")"); + } + } + return null; + } +}