California oak woodland - Photo credit: John Game


General Consortium News


  October 30, 2017

A second paper has been published by the same UC/JEPS team referenced in a previous news item on this page (April 11, 2017), adding phylogenetic methods to the study of diversity and endemism in the California flora. This novel "spatial phylogenetics" approach makes it possible to evaluate biodiversity from an evolutionary standpoint, including discovering significant areas of neo- and paleo-endemism. Read the open-source paper here.


  April 11, 2017

A new study published by a UC/JEPS team uses distributional data from the CCH and other data portals, diversity metrics, and a randomization test, to map biodiversity and endemism for California native vascular plants. These data are available for research use and includes standardized location and collector names that are not yet avaliable on the CCH. Please see summary here, PDF of full paper here, and online version here.


  January 28, 2016

Article describing the value of CCH published in Fremontia


  January 22, 2016

CCH records used in major climate change study on the California Flora
Coverage by Climate Central: Climate Change Is Leaving Native Plants Behind


  February 18, 2015

CCH now serving data from 2 million specimens!
Coverage by CDL: The Consortium of California Herbaria (CCH) has its roots in the California Digital Library (CDL)
Coverage by UCNRS: Digital California plant portal hits 2 million specimens


  November 14, 2014

CCH included in Google Analytics study of plant data websites


  July 7, 2013

Article in Chico Statements about innovative operation of Chico Herbarium


  May 3, 2012

Newspaper article about HSU's digitization effort


  June 24, 2008

Botanical refugees: Climate change paper using Consortium data published in PLOS ONE


  September 5, 2008

Botanizing California: A visualization of the history of California botanical collection from the Spatial History group at Stanford using CCH data



Updates News

Updates for 2017

  October 27  —  RSA updated

  1. RSA/POM   The new Specify database has been fully processed into CCH. No longer will data from the old filemaker database be processed into CCH. The error from last week affecting the results of family searches has been fixed by loading this new database file.
Cleanup and reassignment of the georeference records for this change is ongoing. More orphaned georeferences were corrected to the new accession numbers in this refresh. There are ones that are still problematic. The georeferences are being checked for yellow flags and changed when necessary.

  2. RSA/POM   The bug present in the previous refresh that added erroneous RSA/POM records into family searches appears to have been fixed with the use of the new database file.

   1052424 Records with decimal Lat/Long, processed from coordinates on the label.
    630346 georeference records from the Primary Buffer.
     81954 georeference records from the Baldwin et al 2017.
       3387 georeference records from other user submitted files.
       3444 georeference records from the Mexico buffer.
    129856 yellow-flagged georeference records

   Record count: 2,275,718 (1,772,217 of which are georeferenced)


  October 25  —  Bug fixes, no updates

  1. Fixed a bug where the data was not being created correctly for the GBIF IPT port of the CCH data. Fixed a bug where new records and new determinations were not displaying in the html pages accurately.

  2. RSA/POM   A bug is still present where certain small subset of specimens are displaying in the wrong family when only a family is searched.

  In general, this update removed additional records from some collections that had missing data in all but the state field. Also some additional specimens from outside the CA-FP boundary in Mexico (mostly with unknown in the municipality field) were removed from display in the CCH. David set these specimens up to be included but because the georeferences were outside the CA-FP, the coordinates were nulled. These records are now being excluded from CCH so they are not confused with specimens within the CA-FP Mexico boundary that have not been georeferenced.

   1044354 Records with decimal Lat/Long, processed from coordinates on the label.
    630494 georeference records from the Primary Buffer.
     81954 georeference records from the Baldwin et al 2017.
       3387 georeference records from other user submitted files.
       3444 georeference records from the Mexico buffer.
    129522 yellow-flagged georeference records

   Record count: 2,296,109 (1,769,041 of which are georeferenced)


  October 5  —  Bug fixes, no updates

  1. CAS   Fixed a bug that deleted locations from some records

  2. RSA/POM   Deleted some poorly converted special characters in the county field causing probems with the search page

  3. UCR   Fixed a bug with the julian dates used for the search field not being formatted correctly

   1048966 Records with decimal Lat/Long, processed from coordinates on the label.
    630425 georeference records from the Primary Buffer.
     81927 georeference records from the Baldwin et al 2017.
       3387 georeference records from other user submitted files.
       3674 georeference records from the Mexico buffer.
    129522 yellow-flagged georeference records

   Record count: 2,296,109 (1,769,041 of which are georeferenced)

  October 2  —  HSC, HUH, JOTR, OBI, and SBBG updated

  1. RSA POM   A new database refresh is still being processed. This new dataset eliminates the old filemaker program and has all specimens from California in the Specify database. A future refresh will include these data and include a refresh of the Mexico specimens. As with CAS, the primary record number will be changed for RSA and POM once these new data are loaded. The old RSA and POM accession number will be included as an other record number once these data are online.

  To avoid the issue with the CAS georeference buffer, the georeference buffer records using the old RSA/POM accessions will retained until the RSA file has been completely re-formatted and processed. Conversion of the georeference buffer, linking the old accession numbers to the new ones, is ongoing simultaneously. When the new RSA data is live, the successfully converted georeferences in the buffer will also be live.

  2. CAS   Around 200,000 more georeferences from the buffer have been added to this refresh. The buffer georeferences using the old CAS and DS accession number were linked to the new accession number and loaded into this refresh. Most, but not all, georeferences were linked to the new record numbers. There were some that were not found and some that were duplicate accessions. These georeferences were deleted from the buffer.

  3. HUH, CAS, RSA   Due to the time needed for converting the georeference buffer, character formatting errors are still present in these datasets (fractions , degrees, peoples names with special characters, etc displaying as unintelligible character strings). I will be working on correcting these over the next month.

  4. Missing records   Due to new specimen records and recent revisions of the taxon tables, there are ~5000 specimens across all recently updated collections that are currently being kicked out of the loading process due to the names being misspelled or unpublished. This backlog is larger than in the past due to the cleaning up of the taxon tables. Fixing these problem names is a slow process that is being worked on periodically. Many of these names also are cultivated taxa not yet in the taxon table. If there are records for a taxon that were online previously and now are not, please e-mail me. I can find why the record is being kicked out of the loading process and fix the problem before for the next refresh.

  5. Image records   This feature has not been updated since 2015, when David Baxter removed most image record links. The links for most of the image records submitted in recent database updates have been restored. The entire image file had to be recreated and revised. The image links for UC and JEPS specimens are still broken and need to be reformatted again. Currently there are over 50,000 image links in the database, but over 30,000 of those are from SEINET.

Georeference file buffer report:
   876103 Records with decimal Lat/Long, processed from coordinates on the label.
    634206 georeference records from the Primary Buffer.
    194580 georeference records from the Baldwin et al 2017.
       3925 georeference records from other user submitted files.
       6792 georeference records from the Mexico buffer.
    122083 yellow-flagged georeference records


   Record count: 2,295,729 (1,716,268 of which are georeferenced)




  August 14

  1. RSA POM Fixed bug in scripts showing incorrect combined collectors when only a single collector present. This bug appears to have been in the loading script for some time and has escaped detection. Fixed a bug in the script that was deleting the subtaxon names of specimens loaded from the Filemaker pro version of the data. More records from RSA and POM are present in this refresh than in the last couple refreshes.
Georeference file buffer report:
  1039322 Records with decimal Lat/Long, processed from coordinates on the label.
    474149 georeference records from the Primary Buffer (including Baja).
      76413 georeference records from the Baldwin et al 2017.
       9254 georeference records from other user submitted files.
    117242 yellow-flagged georeference records


   Record count: 2,289,947 (1,599,967 of which are georeferenced)




  August 8  —  CAS-BOT-BC and SJSU updated

  1. CAS-BOT-BC (formerly CAS and DS) has been revised further. The error that resulted in mis-mapping of a majority of CAS specimens in the July refresh has mostly been fixed. As a result of the new herbarium code and barcode numbers, no georeference buffer records cannot be applied to this collection at this time. Therefore, there are 200,000+ records that are not georeferenced in this refresh that were mapped in July.
A GIS-based fix for mapping the buffer coordinates (which use the old accession numbers) to the new herbarium codes is underway. Most of the georeference buffer coordinates should be salvageable. There will be a considerable number of specimens left without coordinates after this fix. These are old duplicate accessions that were kicked out previously, that after the change in herbarium codes, are now newly displayed on the CCH.
  2. More coordinates and specimens from CHSC and RSA/POM were added due to further revisions of the loading scripts. The loading scripts for these three herbaria will be completely updated by the end of August. This is a complicated process and if you see any errors or problems, please let us know.


Georeference file buffer report:
  1039315 Records with decimal Lat/Long, processed from coordinates on the label.
    474040 georeference records from the Primary Buffer (including Baja).
      76419 georeference records from the Baldwin et al 2017.
       9251 georeference records from other user submitted files.
    117242 yellow-flagged georeference records


   Record count: 2,289,071 (1,599,853 of which are georeferenced)



  July 24 — CAS and DS (as CAS-BOT-BC), SCFS, SDSU, UCSC, and UCD updated

  1. The loading scripts for CDA, CHSC, and RSA/POM were partially updated to the new version. Only a small proportion of the georeferenced specimens were being mapped online since April (only those records that had just decimal latitude and longitude as coordinates). The problem has now been corrected. The loading scripts for these three herbaria will be completely updated in August. This is a complicated process and if you see any errors or problems, please let us know.

  2. CAS/DS is now known as CAS-BOT-BC, as a result of their changeover to a Symbiota-based database. The new herbarium code and accessions in their recent update have overwritten all of the old accessions present in the previous versions of CCH. Additional fixes are underway to show the old CAS & DS accessions on the Accession Detail Results pages.

  3. A major update of the SEINET records from California were added in this refresh. The new upload includes many more specimen records (over 123,000 records) and herbaria than included previously. The SEINET loader has been updated to the current format.

  4. Specimen records and georeferences from two new field station herbaria have been added to the CCH. Specimens from BRFS (Blodgett Forest Research Station) and HREC (Hopland Research and Extension Center) were imaged and databased at UC-JEPS and will continue to be uploaded when the UC-JEPS data are refreshed.

  5. Specimen records and georeferences from the Sagehen Creek Field Station herbarium (SCFS) have been added to the CCH.

  6. Cleanup of the georeference buffer is mostly complete. The remaining georeference coordinates missing in the past update are present in this one. A previous issue with the georeferenced records from the Baldwin et al. 2017 study (see April 11, 2017 news above) overwriting georeferences from the primary buffer was corrected.
Georeference file buffer report:
  1359762 Records with decimal Lat/Long, processed from coordinates on the label.
    400257 georeference records from the Primary Buffer (including Baja).
      64340 georeference records from the Baldwin et al 2017.
      10974 georeference records from other user submitted files.


   Record count: 2,250,827 (1,833,380 of which are georeferenced)



  April 27 —
  Cleanup of the georeference buffer is mostly complete. The remaining georeference coordinates missing in the past update are present in this one.

  Baja California records without coordinates now will show up in the CCH. These were being removed by scripts in previous updates. There are a little over 6700 Baja records without georeferences, some of which are being georeferenced by CONABIO via a grant with the UC-JEPS Herbarium.

  There is still a problem with Baja California records with "unknown" municipality not being able to be distinguished from California records with "unknown" county. This is due to the lack of a Country Field. This is currently being worked on and will be enabled in a future update.

   Record count: 2,168,516 (1,602,859 of which are georeferenced)



  April 18 — BLMAR, JROH, GMDRC, SD, UCR Updated
  A revision of the data loading scripts of the above 4 participants plus CATA is complete. Phenology, habitat, associates, and other voucher data should now be displaying for these herbaria when present. Additional updates to several other herbaria are in process. If you see any errors or problems, please let us know.   Cultivated Specimens are now fully included in CCH Queries, but Phase Two (ability to choose to not query cultivated specimens) is not yet implemented
  Cleanup of data, yellow flagging, and georeferenced coordinates is ongoing. Due to some changes with the georeferencing buffer process, the total georeferenced specimens is lower this update. More cleanup of the georeference buffer is planned and additional georeference coordinates will re-appear in a future update
  Additional Baja California records now have geocoordinates due to the georeferencing efforts of Jon Rebman and the SDNHM.

   Record count: 2,161,735 (869,111 of which are georeferenced)

Updates for 2016

  Dec 20 — JROH Updated
  general error and bug corrections were completed to restore the CCH after data server was taken offline in November

Record count: 2,149,422 (1,604,019 of which are georeferenced)


  Sep 12 — UCR Updated
  CCH welcomes the Inyo National Forest Herbarium (INF) in Bishop as a data provider
  The import of INF records are not yet complete, but should be next year (2017).

Record count: 2,149,422 (1,604,019 of which are georeferenced) Sep 12


  May 27 — JROH, SBBG, SD, SEINET, SJSU Updated
  Now serving CFP Baja records from CAS, RSA, UC, UCR

Record count: 2,147,910 (1,602,611 of which are georeferenced) May 27


  Apr 29 — CDA, UCD Updated

Record count: 2,117,834 (1,590,310 of which are georeferenced) April 29


  Apr 25 — RSA, UCSB Updated

Record count: 2,100,600 (1,584,284 of which are georeferenced) April 25


  Feb 17 — CAS, SDSU Updated

Record count: 2,090,128 (1,567,691 of which are georeferenced) February 17


  Feb 5 — GMDRC, HSC Updated

Record count: 2,082,115 (1,561,092 of which are georeferenced) February 5


  Jan 26 — CLARK, UCR Updated

Record count: 2,078,164 (1,559,109 of which are georeferenced) January 26


  Jan 19 — JROH Updated

Record count: 2,076,744 (1,557,827 of which are georeferenced) January 19


  Jan 11 — UCSC, OBI Updated

Record count: 2,076,532 (1,557,657 of which are georeferenced) January 11


Updates for 2015

  Oct 23 — CATA, SD Updated

Record count: 2,069,584 (1,540,764 of which are georeferenced) October 23


  Oct 2 — UCR Updated

Record count: 2,065,567 (1,539,152 of which are georeferenced) October 2


  Sept 21 — JROH, SJSU Updated

Record count: 2,060,073 (1,531,239 of which are georeferenced) September 26


  Aug 3 — CHSC, UCSC Updated

Record count: 2,058,967 (1,521,914 of which are georeferenced) August 26


  Jun 26 — CAS Updated

Record count: 2,054,347 (1,487,129 of which are georeferenced) June 26


  Jun 22 — RSA Updated

Record count: 2,023,297 (1,470,818 of which are georeferenced) June 22


  May 8 — SD Updated

Record count: 2,015,927 (1,458,827 of which are georeferenced) May 8


  Apr 21 — CCH welcomes California State University, Fullerton (MACF) as a data provider

Record count: 2,013,018 (1,452,633 of which are georeferenced) April 21


  Apr 10 — SBBG, UCD Updated

Record count: 2,012,323 (1,449,361 of which are georeferenced) April 10


  Apr 3 — CCH welcomes the Catalina Island Conservancy (CATA) as a data provider

Record count: 2,008,768 (1,440,373 of which are georeferenced) April 3


  Mar 10 — HSC Updated

Record count: 2,006,122 (1,433,229 of which are georeferenced) March 10


  Feb 13 — JROH, SJSU Updated

Record count: 2,003,287 (1,421,616 of which are georeferenced) February 13


  Feb 6 — SEINET Updated
  CCH welcomes Sweeney Granite Mountains Desert Research Center (GMDRC) as a data provider,
  putting CCH over two million specimen records!

Record count: 2,002,998 (1,417,708 of which are georeferenced) February 6


  Jan 16 — HUH Updated

Record count: 1,986,263 (1,402,942 of which are georeferenced) January 16


Updates for 2014

  Dec 19 — UCR Updated

Record count: 1,985,750 (1,394,920 of which are georeferenced) December 19


  Nov 21 — RSA/POM, SD Updated

Record count: 1,982,606 (1,377,544 of which are georeferenced) November 21


  Nov 7 — UCR Updated

Record count: 1,977,167 (1,365,813 of which are georeferenced) November 7


  Oct 31 — UCSB, YM Updated

Record count: 1,975,617 (1,360,603 of which are georeferenced) October 31


  Oct 24 — VVC Updated

Record count: 1,962,685 (1,355,156 of which are georeferenced) October 24


  Oct 17 — SD Updated

Record count: 1,962,151 (1,350,004 of which are georeferenced) October 17


  Sept 26 — CLARK, UCD Updated. UCD now serving determination history

Record count: 1,959,970 (1,326,749 of which are georeferenced) September 26


  Sept 12 — OBI, CAS Updated

Record count: 1,956,852 (1,324,332 of which are georeferenced) September 12


  Sept 5 — CCH welcomes Pasadena City College Herbarium (PASA) as a data provider

Record count: 1,949,558 (1,317,943 of which are georeferenced) September 5


  Aug 8 — UCR now serving determination history and specimen images

Record count: 1,947,092 (1,287,777 of which are georeferenced) August 8


  Aug 1 — SJSU Updated

Record count: 1,947,071 (1,278,463 of which are georeferenced) August 1


  Jul 25 — CLARK, SDSU, UCR Updated

Record count: 1,946,867 (1,271,048 of which are georeferenced) July 25


  Jun 26 — CAS Updated

Record count: 1,942,879 (1,239,719 of which are georeferenced) June 26


  May 23 — HUH Updated

Record count: 1,923,306 (1,219,196 of which are georeferenced) May 23


  Apr 4 — RSA Updated

Record count: 1,922,851 (1,200,778 of which are georeferenced) April 4


  Mar 27 — UCR Updated

Record count: 1,919,553 (1,193,662 of which are georeferenced) March 27


  Mar 21 — CHSC Updated

Record count: 1,915,935 (1,185,625 of which are georeferenced) March 21


  Mar 7 — SD Updated

Record count: 1,915,419 (1,172,550 of which are georeferenced) March 7


  Feb 28 — SBBG Updated

Record count: 1,914,499 (1,167,007 of which are georeferenced) February 28


  Feb 14 — Jasper Ridge Biological Preserve at Stanford University (JROH) welcomed as a data provider.

Record count: 1,913,541 (1,151,950 of which are georeferenced) February 14


  Jan 31 — UCSB Updated

Record count: 1,909,005 (1,140,556 of which are georeferenced) January 31


  Jan 24 — SD, HUH Updated

Record count: 1,903,565 (1,136,808 of which are georeferenced) January 24


  Jan 17 — DAV Updated

Record count: 1,900,235 (1,131,436 of which are georeferenced) January 17


  Jan 10 — CAS, UCLA Updated

Record count: 1,891,361 (1,127,630 of which are georeferenced) January 10

See the CCH Update History page for earlier updates.

  Copyright © 2017 Regents of the University of California — Updated October 30, 2017