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SemMedDB Database Download

We have archived versions 31, 40, and 41 of the SemMedDB database.

On March 3 2022, we will permanently delete them.

If they are still needed, please e-mail us at semmed@nlm.nih.gov.

The databases downloadable here (from version 3.0 on) have been created using the new database schema (The schema and database information is available here).

Note that the database file named "WHOLEDB" contains the entire database except the ENTITY table, which the new database provides. The individual tables are also provided separately. Users can download the entire database at once or the individual tables separately depending on their needs. The file names consist of four parts: database name _ R (or A) _ table name _ PubMed to date. The letter R represents that the database was generated with standard SemRep options, whereas A denotes that it was generated with the anaphora resolution option.

The new database schema differs from the previous one (versions 2X) in the following ways:

  1. We simplified the schema significantly by removing the CONCEPT, CONCEPT_SEMTYPE, PREDICATION_ARGUMENT, and SENTENCE_PREDICATION tables. The relevant contents of these tables can still be derived from PREDICATION if needed.
  2. A GENERIC_CONCEPT table has been added to the schema. This table contains generic concepts, as indicated by SemRep. The concepts that are not in this table are considered novel.
We no longer produce an annual release of the database of predications generated by SemRep using the sortal anaphora resolution. For sortal anaphora resolution in SemRep, see our BMC Bioinformatics paper.

The GENERIC_CONCEPT table has been updated in the June 30 2018 and all subsequent releases. Consequently, the SUBJECT_NOVELTY and OBJECT_NOVELTY columns of the PREDICATION table have been updated as follows: If the concept is not in the GENERIC_CONCEPT table, the value is set to 1; otherwise, it is set to 0.

Starting with version VER40, the PMID column in SENTENCE is dependent on the PMID in the CITATION table with a foreign key constraint. Therefore, all the PMIDs in the SENTENCE table have corresponding rows in the CITATION table, which has metadata PMID information.


Please note that all downloads in the tables below require a UMLS Terminology Services (UTS) account; to sign up for a UTS account, please click here.

Database name: semmedVER43_R (Processed using MEDLINE BASELINE 2020 + Covid-19 citations + PubMed Update Files through April 9, 2021 ) New Item

Semrep version: Regular semrep version 1.8
Number of citations processed: 32,385,448
Number of predications: 111,493,072
* This database was obtained from SemRep results with the anaphora feature turned off.

The next table contains links to MySQL download files.
TABLE NAME Size # Rows Download linksha1summd5sum
Entire Database 20G  N/A  download download download
CITATIONS 152M  32,385,448  download download download
ENTITY 37G  1,547,524,522  download download download
GENERIC_CONCEPT 4.7K  259  download download download
PREDICATION 2.7G  111,493,072  download download download
PREDICATION_AUX 3.4G  111,493,072  download download download
SENTENCE 13G  218,225,579  download download download


The next table contains links to CSV files (there is no CSV file for the Entire Database).
TABLE NAME Size # Rows Download linksha1summd5sum
CITATIONS 152M  32,385,448  download download download
ENTITY 38G  1,547,524,522  download download download
GENERIC_CONCEPT 3.9K  259  download download download
PREDICATION 2.7G  111,493,072  download download download
PREDICATION_AUX 3.6G  111,493,072  download download download
SENTENCE 14G  218,225,579  download download download


Database name: semmedVER42_R (Processed using MEDLINE BASELINE 2020 + Covid-19 citations)
semmedVER42_R is a superset of semmedVER41_R (which included the entire 2020 Baseline) that includes in addition data derived from all PubMed citations obtained using the query

( covid OR sars-cov-2 OR wuhan OR coronavirus OR 2019-ncov OR sars ) AND 2019:2020[dp]
The additional Covid citations were processed with SemRep and the 2020AA UMLS data, which includes Covid-19 terms in CUIS C5203670, C5203671, C5203672, C5203673, C5203674, C5203675, and C5203676.
Semrep version: Regular semrep version 1.8
Number of citations processed: 30,454,210
Number of predications: 103,284,300
* This database was obtained from SemRep results with the anaphora feature turned off.

TABLE NAME Size # Rows Download linksha1summd5sum
Entire Database 18G  N/A  download download download
CITATIONS 142M  30,439,312  download download download
ENTITY 33G  1,369,836,547 download download download
GENERIC_CONCEPT 4.7K  259  download download download
PREDICATION 2.5G  103,284,300  download download download
PREDICATION_AUX 3.1G  103,208,390  download download download
SENTENCE 12G  199,843,876  download download download


 
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Last Modified: April 11, 2021    Server: ii-public1
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