Version 2.0.0

What's Changed (Aug 31, 2024)

1. Data Updates in Alzkb:

   • DrugBank: Updated to version 5.1.12 (2024-03-14)
   • NCBI Gene: Updated to V2024-05-13
   • Gene Ontology: Updated to V2024-04-24*
   • MESH: Updated to V2023-12*
   • Uberon: Updated to V2024-03-22*
   • DrugCentral: Updated to V2023-11-01*
   • BindingDB: Updated to V2024-05*
   • MEDLINE: Updated to V2024-05-02*
     *Updates based on Hetionet. Please see the alzkb-updates Github repository for more details.

2. Enhancements:

   • Added TranscriptionFactor nodes and TRANSCRIPTIONFACTORINTERACTSWITHGENE relationships.

   • Added chromosome number as a property to gene nodes.

   • Added sourcedatabase as properties to nodes.

   • Added correlation, score, p_fisher, z_score, affinity_nm, confidence, sourcedatabase, and unbiased, from Hetionet, DisGeNET, and DoRothEA as properties to relationships.

     Relationships	Properties
     CHEMICALBINDSGENE	['sourceDB', ' unbiased', ' affinity_nM']
     CHEMICALDECREASESEXPRESSION	['sourceDB', ' unbiased', ' z_score']
     CHEMICALINCREASESEXPRESSION	['sourceDB', ' unbiased', ' z_score']
     DISEASELOCALIZESTOANATOMY	['sourceDB', ' unbiased', ' p_fisher']
     GENEASSOCIATESWITHDISEASE	['sourceDB', ' score']
     GENECOVARIESWITHGENE	['sourceDB', ' unbiased', ' correlation']
     SYMPTOMMANIFESTATIONOFDISEASE	['sourceDB', ' unbiased', ' p_fisher']
     TRANSCRIPTIONFACTORINTERACTSWITHGENE	['sourceDB', ' confidence']

   The instructions for adding new data resources and importing data to the Memgraph graph database are available at alzkb Github repository.

3. Data Quality Improvements:

   • Removed the mapping between Creutzfeldt-Jakob disease (CJD) and Familial Alzheimer Disease (FAD). CJD and FAD are different diseases but got merged to the same node in AlzKB because of the DisGeNET “disease_mappings.tsv” file, in which CJD is mapped to FAD.
   • Filtered genes to keep human genes only (tax-id = 9606).
   • Implemented case-insensitive matching when extracting Alzheimer’s data from DisGeNET to include disease names that are in all caps.
   • Consolidated pathways with the same names but different values of pathwayid and sourcedatabase.
   • Removed duplicated pathways from AOP-DB that have “Homo sapiens (human)” in their names.
   • Removed 21,724 Drug nodes from AOP-DB that had only xrefmesh values and NULL as commonName and were not connected to any other nodes.

Summary of the changes in nodes and relationships
Nodes:

Label	NodeCount	NodeCount previous version	NumChanges
BiologicalProcess	12322	11381	941
BodyPart	652	402	250
CellularComponent	1695	1391	304
Disease	34	20	14
Drug	16581	36959	-20378
DrugClass	474	345	129
Gene	193279	193313	-34
MolecularFunction	3460	2884	576
Pathway	4516	4570	-54
Symptom	505	438	67
TranscriptionFactor	519		519
Total	234037	251703	-17666

Relationships:

Type	RelCount	RelCount previous version	NumChanges
BODYPARTOVEREXPRESSESGENE	97772	97772	0
BODYPARTUNDEREXPRESSESGENE	102185	102185	0
CHEMICALBINDSGENE	25726	11531	14195
CHEMICALDECREASESEXPRESSION	21051	21051	0
CHEMICALINCREASESEXPRESSION	18713	18713	0
DISEASELOCALIZESTOANATOMY	33	29	4
DRUGCAUSESEFFECT	2	2	0
DRUGINCLASS	1945	1029	916
DRUGTREATSDISEASE	9	9	0
GENEASSOCIATEDWITHCELLULARCOMPONENT	88880	73553	15327
GENEASSOCIATESWITHDISEASE	508	502	6
GENECOVARIESWITHGENE	61606	61606	0
GENEHASMOLECULARFUNCTION	104752	97191	7561
GENEINPATHWAY	178991	179433	-442
GENEINTERACTSWITHGENE	147088	147001	87
GENEPARTICIPATESINBIOLOGICALPROCESS	548285	559385	-11100
GENEREGULATESGENE	263978	265667	-1689
SYMPTOMMANIFESTATIONOFDISEASE	53	79	-26
TRANSCRIPTIONFACTORINTERACTSWITHGENE	6910		6910
TOTAL	1668487	1636738	31749

The full database dump can be downloaded from the following link: https://cedars.box.com/v/alzkb-v2-0-0

Instruction for Installing from the CYPHERL file can be found here.

Version 1.2.1

What's Changed (May, 2024)

• Migrated Alzkb from Neo4j to Memgraph 2.17.0.

The full database dump can be downloaded from the following link: https://cedars.box.com/v/alzkb-v1-2-1

Instruction for Installing from the CYPHERL file can be found here.

Version 1.2.0

What's Changed (Jan 24, 2024)

• Modified the graph schema adding two new relationship types between genes (imported from Hetionet): geneCovariesWithGene and geneRegulatesGene.
• Updated AlzKB with recent NCBI Gene data (2023-11-09).

Summary of the changes in nodes and relationships

Node (208,436 --> 251,704):

• Gene: 150,045 --> 193,313

Relationship (1,309,466 --> 1,636,739):

• geneCovariesWithGene: 61,606
• geneRegulatesGene: 265,667

The full database dump can be downloaded from the following link:
https://upenn.box.com/s/jmnlcc3zk9yzclky0uv8dd9q7nkxmcgm
or
https://cedars.box.com/v/alzkb-v1-2-0

Version 1.1.0

What's Changed (Aug 2, 2023)

• Updated the AlzKB with the most recent DrugBank data (V5.1.10 that was released on 2023-01-04) and NCBI Gene data (2023-05-03).
• Upgraded AlzKB to neo4j version 5.

Summary of the changes in nodes and relationships
Node (118,902 --> 208,436):

• Gene: 62407 --> 150045 (geneAssociatesWithDisease doesn't change)
• Drug from drug bank: 13339 --> 15235 (Drug 35063 -->36959)

Relationship (1,309,527 --> 1,309,466):

• bodyPartOverexpressesGene: 97782 --> 97772
• bodyPartUnderexpressesGene: 102194 --> 102185
• geneInPathway: 179464 --> 179433
• geneInteractsWithGene: 147008 --> 147001
• geneParticipatesInBiologicalProcess: 559389 --> 559385

The full database dump can be downloaded from the following link:
https://cedars.box.com/v/epistasislab-alzkb-v1-1-0

AlzKB first DOI release

This is a duplicate of the first release of AlzKB at https://github.com/EpistasisLab/AlzKB/releases/tag/v1.0.0 .

Version 1.0.0

This is our initial release of AlzKB!

The full database dump can be downloaded from the following link:
https://upenn.box.com/s/dalcofa8i7rkkc2h2n6bfg8nvmwi83pq
or
https://cedars.box.com/v/epistasislab-alzkb-v1-0-0

Advanced users have the option of building the database from scratch, although we are still working on finishing the documentation for this procedure..