mysql> show tables;

The Namespace Table – Specific Types, Access, Global Connectivity Constraints.

Table description

mysql> describe namespace;

+------------------+-------------+------+-----+---------+-------+

+------------------+-------------+------+-----+---------+-------+

+------------------+-------------+------+-----+---------+-------+

4 rows in set (0.00 sec)

Example

mysql> select * from namespace order by idtype limit 5;

+-----------------------------------------+-------------------------------------------+------------+-----------+

+-----------------------------------------+-------------------------------------------+------------+-----------+

…

+-----------------------------------------+-------------------------------------------+------------+-----------+

5 rows in set (0.00 sec)

The Relevancy Table – Type Groupings Relevant to Semantic Types.

Table description

+---------+------+------+-----+---------+-------+

+---------+------+------+-----+---------+-------+

+---------+------+------+-----+---------+-------+

| genesymbol | (hugo_hgnc_officialsymbol_uid hugo_hgnc_aliassymbol_annot ncbi_ll_aliasprotien_annot ncbi_ll_aliassymbol_annot ncbi_ll_officialsymbol_annot ncbi_ll_preferredsymbol_annot stanford_spd_officialsymbol_annot |

| genename | (hugo_hgnc_officialname_annot um_bbd_enzyme_annot ncbi_ll_aliasname_annot ncbi_ll_officialname_annot ncbi_ll_aliasname_annot ncbi_ll_preferredname_annot stanford_sgd_genename_annot) |

| gene | (affymetrix_netaffyx_affyprobe_uid ebi-sib_trembl-sp_p_acc ebi-sib_trembl-sp_p_uid ebi_trembl_p_acc ebi_trembl_p_uid gu_pir_p_uid hugo_hgnc_officialsymbol_uid jax_mgd_gene_uid ncbi_genbank_p_acc ncbi_genbank_p_uid ncbi_ll_aliasprotien_annot ncbi_ll_aliassymbol_annot ncbi_ll_locus_uid ncbi_ll_officialsymbol_annot ncbi_ll_preferredsymbol_annot ncbi_refseq_np_uid ncbi_refseq_xm_acc ncbi_refseq_xm_uid ncbi_refseq_xp_acc ncbi_refseq_xp_uid

…

| officialsymbol | (hugo_hgnc_officialsymbol_uid ncbi_ll_officialsymbol_annot stanford_spd_officialsymbol_annot ut-ca_bind_officialsymbol_annot)

The Fact Tables - Identifiers and Fact Registration. Specific Connectivity Constraints.

Table description

mysql> describe HumanFacts;

+------------+-------------+------+-----+---------+-------+

+------------+-------------+------+-----+---------+-------+

+---------------------------------------------------------+

Example

+--------------+--------------------+--------------------------------+------------+------------+------------+-----------+

+--------------+--------------------+--------------------------------+------------+------------+------------+-----------+

| nuid-2072786 | 7340969 | ncbi_genbank_n_uid | NCBI-LL | NULL | 0 | nil |

| nuid-2215370 | 22761563 | ncbi_genbank_n_uid | NCBI-LL | NULL | 0 | nil |

| nuid-767613 | Q8N9J3 | sib_swissprot_p_acc | AFFYMETRIX | NULL | 0 | nil |

| nuid-2384655 | FLJ13556 | ncbi_ll_aliassymbol_annot | NCBI-LL | NULL | 0 | nil |

| nuid-2544940 | AAH09326 | ncbi_genbank_p_acc | NCBI-LL | NULL | 0 | nil |

| nuid-4428303 | 51475048 | ncbi_genbank_contig_uid | NCBI-LL | nil | 3324241944 | t |

| nuid-4428310 | 3610142 | ncbi_pubmed_literature_uid | NCBI-LL | nil | 3324228940 | t |

…

7 rows in set (0.01 sec)

The Map Tables – Method, Time of Linking, Source and linkages to Registered Facts.

Table description

mysql> describe HumanMaps;

+--------+-------------+------+-----+---------+-------+

+--------+-------------+------+-----+---------+-------+

+--------+-------------+------+-----+---------+-------+

5 rows in set (0.01 sec)

Example

+--------------+-------------+------+---------------------------+-----------+

+--------------+-------------+------+---------------------------+-----------+

| muid-2118263 | 4572462 | nil | ncbi-ll-tmpl-parse-Hs | 599223651 |

| muid-1255565 | 71285_at | nil | affymetrix-Hs-annot-parse | 535646377 |

| muid-1285564 | Hs.368007 | nil | affymetrix-Hs-annot-parse | 535801118 |

| muid-1585604 | BAB14925 | nil | ncbi-ll-tmpl-parse-Hs | 597552731 |

| muid-1825598 | 1524068 | nil | ncbi-ll-tmpl-parse-Hs | 598140408 |

| muid-2718208 | NG_002676 | nil | ncbi-ll-tmpl-parse-Hs | 600301027 |

| muid-1224916 | 62274_at | nil | affymetrix-Hs-annot-parse | 535486389 |

| muid-1284913 | AA174142 | nil | affymetrix-Hs-annot-parse | 535798748 |

…

+--------------+-------------+------+---------------------------+-----------+

The Graph Table – Normalized Fact linkages referenced by Method.

Table description

mysql> describe HumanGraphs1;

+-------+-------------+------+-----+---------+-------+

+-------+-------------+------+-----+---------+-------+

+-------+-------------+------+-----+---------+-------+

2 rows in set (0.00 sec)

Example

mysql> select * from HumanGraphs1 limit 15;

+--------------+--------------+

| muid | nuid |

+--------------+--------------+

| muid-2636134 | nuid-2636080 |

| muid-2636134 | nuid-2636081 |

| muid-2636134 | nuid-2636082 |

| muid-2636134 | nuid-2636083 |

| muid-2636134 | nuid-2636084 |

| muid-2636134 | nuid-2636085 |

| muid-2636134 | nuid-2636086 |

| muid-2636134 | nuid-2636087 |

| muid-2636134 | nuid-2636088 |

| muid-2636134 | nuid-2636089 |

+--------------+--------------+

15 rows in set (0.03 sec)

Appendix 1. Registered Fact Types.

+-----------------------------------------+------------------------------------------

| idtype | typeddescription |

+-----------------------------------------+-------------------------------------------

| affymetrix_netaffyx_affyprobe_uid | Affymetrix affyprobe |

| affymetrix_netaffyx_chip_annot | Affymetrix Chip |

| biobase_transfac_domain_annot | BIOBASE transfac domain |

| biobase_transfac_domain_uid | BIOBASE transfac domain |

| chs-fitzimmons_vh-dissector_anatomy_uid | Center for Human Simulation Anatomy model|

| doe-mbi-ucla_dip_pxp_uid | DOE-MBI-UCLA DIP protein interaction |

| doe-mbi-ucla_dip_p_uid | DOE-MBI-UCLA DIP protein id |

| ebi-sib_trembl-sp_p_acc | EBI-SIB trembl-sp protein |

| ebi-sib_trembl-sp_p_uid | EBI-SIB trembl-sp protein |

| ebi_interpro_domain_uid | EBI domain |

| ebi_interpro_pfam_uid | EBI interpro protein family |

| ebi_interpro_p_uid | EBI interpro protein |

| ebi_trembl_p_acc | EBI trembl protein |

| ebi_trembl_p_uid | EBI trembl protein |

| embl_hssp_structure_uid | EMBL homology-structure id |

| embl_smart_pfam_uid | EBI smart protein family |

| flybase_flybase_gene_uid | Flybase gene |

| germonline_germonline_pathway_uid | UofBasel-ch germonline pathway |

| goc_go-bp_concept_uid | GO consortium biological process uid |

| goc_go-bp_term_annot | GO consortium go biological process term|

| goc_go-cc_concept_uid | GO consortium cellular component uid |

| goc_go-cc_term_annot | GO consortium go cellular component term|

| goc_go-mf_concept_uid | GO consortium molecular function uid |

| goc_go-mf_term_annot | GO consortium go molecular function term|

| gu_pirsf_pfam_uid | UofGeorgetown protein super-family |

| gu_pir_p_uid | UofGeorgetown protein |

| hugo_hgnc_aliassymbol_annot | HUGO HGNC alias symbol |

| hugo_hgnc_genbank_acc | HUGO HGNC genbank accession -mixed |

| hugo_hgnc_officialname_annot | HUGO HGNC official gene name |

| hugo_hgnc_officialsymbol_uid | HUGO HGNC official symbol |

| incyte_ypd_p_uid | Incyte yeast protein database |

| inra-fr_prodom_domain_uid | Prodom domain |

| iubmb_ec_p_acc | IUBMB EC protein |

| jax_mgd_gene_uid | MGD gene id |

| jax_mgd_phenotype_uid | Jax MGD phenotype |

| jax_mgi_marker_uid | Jax MGI genetic marker |

| jhu_gdb_orf_uid | Johns Hopkins GDB orf |

| ku_kegg_ligand_annot | UofKyoto ligand |

| ku_kegg_ligand_uid | UofKyoto ligand |

| ku_kegg_pathway_annot | UofKyoto KEGG pathway |

| ku_kegg_pathway_uid | UofKyoto KEGG pathway |

| mips_mips_pxp_uid | Munich MIPS protein interaction |

| ncbi_cdd_domain_acc | NCBI-conserved-domain |

| ncbi_cdd_domain_annot | NCBI-conserved-domain |

| ncbi_cog_pfam_acc | NCBI-COG protein family |

| ncbi_genbank_contig_acc | NCBI-genbank contig |

| ncbi_genbank_contig_uid | NCBI-genbank contig |

| ncbi_genbank_n_acc | NCBI-genbank nucleotide |

| ncbi_genbank_n_uid | NCBI-genbank nucleotide |

| ncbi_genbank_p_acc | NCBI-genbank protein |

| ncbi_genbank_p_uid | NCBI-genbank protein |

| ncbi_gene_gene_uid | NCBI Entrezgene gene uid |

| ncbi_grif_function_annot | NCBI-LocusLink grif |

| ncbi_ll_aliasname_annot | NCBI-LocusLink name alias |

| ncbi_ll_aliasprotien_annot | NCBI-LocusLink protein alias |

| ncbi_ll_aliassymbol_annot | NCBI-LocusLink symbol alias |

| ncbi_ll_go_annot | NCBI-LocusLink gene ontology definition|

| ncbi_ll_grif_annot | NCBI-LocusLink gene reference into function|

| ncbi_ll_loc-map_annot | NCBI-LocusLink map location |

| ncbi_ll_locus_uid | NCBI-LocusLink locus |

| ncbi_ll_officialname_annot | NCBI-LocusLink official name |

| ncbi_ll_officialsymbol_annot | NCBI-LocusLink official symbol |

| ncbi_ll_organism_annot | NCBI-LocusLink organism |

| ncbi_ll_phenotype_annot | NCBI-LocusLink phenotype |

| ncbi_ll_phenotype_uid | NCBI-LocusLink phenotype |

| ncbi_ll_preferredname_annot | NCBI-LocusLink preferred name |

| ncbi_ll_preferredsymbol_annot | NCBI-LocusLink preferred symbol |

| ncbi_ll_summary_annot | NCBI-LocusLink summary |

| ncbi_mmdb_structure_annot | NCBI-MMDB structure |

| ncbi_mmdb_structure_uid | NCBI-MMDB structure id |

| ncbi_omim_gene_uid | NCBI-OMIM |

| ncbi_pubmed_literature_uid | NCBI-pubmed literature |

| ncbi_refseq_nc_acc | NCBI-refseq complete genomic |

| ncbi_refseq_nc_uid | NCBI-refseq complete genomic |

| ncbi_refseq_ng_acc | NCBI-refseq genomic |

| ncbi_refseq_ng_uid | NCBI-refseq genomic |

| ncbi_refseq_nm_acc | NCBI-refseq mRNA |

| ncbi_refseq_nm_uid | NCBI-refseq mRNA |

| ncbi_refseq_np_acc | NCBI-refseq protein |

| ncbi_refseq_np_uid | NCBI-refseq protein |

| ncbi_refseq_xm_acc | NCBI-refseq model mRNA |

| ncbi_refseq_xm_uid | NCBI-refseq model mRNA |

| ncbi_refseq_xp_acc | NCBI-refseq model protein |

| ncbi_refseq_xp_uid | NCBI-refseq model protein |

| ncbi_refseq_xr_acc | NCBI-refseq non-coding RNA |

| ncbi_refseq_xr_uid | NCBI-refseq non-coding RNA |

| ncbi_taxonomy_taxon_uid | NCBI-taxonomy taxon |

| ncbi_ug_orf_uid | NCBI-unigene orf |

| nlm_medline_literature_uid | NLM medline reference |

| null_null_null_null | null tag |

| pasteur-fr_candida_gene_uid | Pasteur-fr candida gene |

| sanger_pfam_pfam_uid | Sanger pfam protein family |

| sanger_wormpep_p_uid | Sanger inst. protein id |

| sib_prosite_domain_acc | SIB prosite domain acc |

| sib_prosite_domain_uid | SIB prosite domain id |

| sib_swissprot_p_acc | Swissprot protein acc |

| sib_swissprot_p_uid | Swissprot protein id |

| sri-carnegie_metacyc_pathway_acc | Stanford-Carnegie metacyc pathway |

| sri-carnegie_metacyc_pathway_annot | Stanford-Carnegie metacyc pathway description|

| stanford_sgd_genename_annot | Stanford SGD genename |

| stanford_sgd_gene_uid | Stanford SPD id |

| stanford_sgd_literature_uid | Stanford SGD literature |

| stanford_sgd_orf_uid | Stanford SGD orf |

| stanford_sgd_phenotype_annot | Stanford SGD phenotype |

| stanford_sgd_summary_annot | Stanford SGD description |

| stanford_smd_expt_uid | Stanford microarray experiment |

| stanford_spd_aliassymbol_annot | Stanford SPD alias gene symbol |

| stanford_spd_genesymbol_annot | Stanford SPD gene symbol |

| stanford_spd_officialsymbol_annot | Stanford SPD official gene symbol |

| tigr_cmr_microbial_uid | TIGR comprehensive microbial |

| tigr_egad_m_uid | TIGR EGAD rna |

| tigr_tgi_orf_uid | TIGR orf |

| tigr_tigrfams_pfam_uid | TIGR pfam |

| ucsd_tc-db_p_uid | UCSD tc-db protein |

| uf-de_euroscarf_strain_uid | UofFrankfurt-de EUROSCARF strain |

| umber-uk_prints_domain_uid | UofManchester domain id |

| umn_cgc_nomenclature_genename_annot | University of Minnesota Caenorhabditus genetics center gene name |

| umn_cgc_nomenclature_genesymbol_annot | University of Minnesota Caenorhabditus genetics center symbol |

| um_bbd_enzyme_annot | UofMichigan biodegredation enzyme |

| um_bbd_enzyme_uid | UofMichigan biodegredation enzyme |

| um_bbd_pathway_annot | UofMichigan biodegredation pathway |

| uniprot_swissprot_genesymbol_annot | Uniprot_swissprot_genesymbol |

| uniprot_swissprot_keyword_annot | Uniprot_swissprot keyword |

| uniprot_swissprot_litdates_annot | Uniprot citation dates |

| uniprot_swissprot_plength_annot | Uniprot protein length |

| uniprot_swissprot_pmw_annot | Uniprot molecular weight |

| uniprot_swissprot_proteinname_annot | Uniprot_swissprot protein name |

| uniprot_swissprot_p_acc | Uniprot_swissprot protein |

| uniprot_swissprot_p_seq | Uniprot_swissprot protein sequence |

| uniprot_swissprot_seqheader_annot | Uniprot_swissprot sequence header |

| uniprot_trembl_genesymbol_annot | Uniprot_trembl_genesymbol |

| uniprot_trembl_go_uid | GO term id |

| uniprot_trembl_keyword_annot | Uniprot_trembl keyword |

| uniprot_trembl_litdates_annot | Uniprot citation dates |

| uniprot_trembl_plength_annot | Uniprot protein length |

| uniprot_trembl_pmw_annot | Uniprot molecular weight |

| uniprot_trembl_proteinname_annot | Uniprot_trembl protein name |

| uniprot_trembl_p_acc | Uniprot_trembl protein |

| uniprot_trembl_p_seq | Uniprot_trembl protein sequence |

| uniprot_trembl_seqheader_annot | Uniprot_trembl sequence header |

| UofW_foundation-anatomy_anatomy_uid | UofW Foundation model of Anatomy id |

| ut-ca_bind_officialsymbol_annot | University of Toronto BIND protein |

| ut-ca_bind_pxp_uid | University of Toronto BIND protein interactioon|

| whitehead-mit_human-snp-db_marker_uid | Mit-whitehead Human SNPs |

| whitehead-mit_mouse-snp-db_marker_uid | Mit-whitehead mouse SNPs |

| wusm-sanger_wormbase_genename_annot | Sanger-WUSM C.elegans coding gene name |

| wusm-sanger_wormbase_genesymbol_annot | Sanger-WUSM C.elegans gene symbol |

| wusm-sanger_wormbase_orf_uid | Sanger-WUSM C.elegans coding sequence [CDS] id|

| wusm-sanger_wormbase_p_acc | Sanger-WUSM C.elegans peptide accession|

| wusm-sanger_wormbase_p_pid | Sanger-WUSM C.elegans peptide id |

+-----------------------------------------+----------------------------------------|

150 rows in set (0.00 sec)

Descriptron’s Relational Backend and Data Model:

Table overview: Data Integation Components

The Namespace Table – Specific Types, Access, Global Connectivity Constraints.

Table description

Example

The Relevancy Table – Type Groupings Relevant to Semantic Types.

Table description

Example

The Fact Tables - Identifiers and Fact Registration. Specific Connectivity Constraints.

Table description

Example

The Map Tables – Method, Time of Linking, Source and linkages to Registered Facts.

Table description

Example

The Graph Table – Normalized Fact linkages referenced by Method.

Table description

Example

Appendix 1. Registered Fact Types.

API Issues

- Simplicity, Flexibility.

- MYSQL/Oracle compatibile.

- Scaleable for large systems.

- Speed.

- Language independent (accessable to all database API’s)

- Updating and Search expressions that overcome combinatorial issues (State vs Path Functions, Two Step algorithm).

- Synchronized with sources

Web Services

WSDL - (Web Services Definition Language) Complete description of a soap (Structured Object Access Protocol) service that provides access to a resource on the internet that can be used in local code.

Soap Service – an interface to a remote resource via XML/SOAP RPC messaging interface with defined inputs and outputs.

Soap Server/Processor - a local computer program that can communicate via the web with XML/Soap Calls.

Workflow – a connected set of processors that combine to perform computational tasks.