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Consortium of California Herbaria (CCH)
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January 1, 2020 Extensive changes to all CCH1 webpages will be completed in stages as the new database is created and populated with data from CCH2. When fully updated with new data from CCH2, some search features currently present may be removed temporarily from the website until bugs can be fixed. Any features taken offline or restored will be listed in the Update News section below. 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
Update News Updates for 2018 September 20 — Last update data to to CCH1. These data are now archived and no longer updated Record count: 2,320,817 (1,778,243 of which are georeferenced) July 12 — SEINET updated; additional error and bug fixes
1093633 Records with decimal Lat/Long, processed from coordinates on the label. June 22 — RSA, SD updated; additional error and bug fixes
1089029 Records with decimal Lat/Long, processed from coordinates on the label. June 07 — SDSU updated; additional error and bug fixes
1084789 Records with decimal Lat/Long, processed from coordinates on the label. May 24 — GMDRC, RSA, SD updated 1. UC/JEPS, CATA, CDA, HUH, HSC, OBI, UCSC. Updated some poorly coverted dates that were causing anomalies in search results.
1080258 Records with decimal Lat/Long, processed from coordinates on the label. March-April — Error and bug fixes 1. Updated some broken collector information links on the Acession Details page. 2. Fixed a long-standing bug that was causing composite collection numbers (for example: 12-134-C, CL-123-35) to display as a long-integer (12134C, CL12335). The number was being reported correctly in database download files in the respective CNUM-prefix, CNUM, and CNUM-suffix fields. However, this was causing confusing results using some of the advanced search features and the sorting function of the search results table, which only uses the CNUM field data for sorting (in these two cases, 134 and 123, respectively). The display has been fixed to show a space between the composite number fields, instead of the former display on an unbroken string of numbers and letters. 3. Sorting the date display on the search results page should now be more intuituive since it is displaying a formatted date, not the verbatim date (or the unfomatted date from the home database). For reference, the unformatted date from the label is displayed on the verbatim date line in the Acession Details page, when present and different from the formatted date. Record count: 2,278,083 (1,777,704 of which are georeferenced)February 23 — minor error and bug fixes 1. Updated the georeference buffer tables to fix some yellow flag errors. 2. Fixed a bug in the synonymy where searches were not returning synonymns in different genera.
3. Fixed a bug where the camera icon for images was not showing up on search results pages. 4. There is still a known bug in a few Packera and Boechera specimens in UC/JEPS that are ID'd
1062158 Records with decimal Lat/Long, processed from coordinates on the label. February 21 — UCD updated 1. VVC Fixed a bug that kicked out most VVC records in the last refresh. 2. Updated the georeference buffer tables to fix some yellow flag errors.
1061980 Records with decimal Lat/Long, processed from coordinates on the label. February 8 — CHSC, VVC updated 1. Updated the georeference buffer tables to fix some yellow flag errors.
1055383 Records with decimal Lat/Long, processed from coordinates on the label. January 26 — JOTR, UCSC updated 1. JOTR Fixed some georeference and species determination errors. 2. UCSC Fixed some errors in the accession number field. 3. Updated the georeference buffer tables to fix some yellow flag errors. 4. Further refinement in this refresh has excluded 2-3,000 more UC-JEPS specimens from Baja that map outside the CA-FP Baja boundary that also have an 'unknown' municipality.
1055066 Records with decimal Lat/Long, processed from coordinates on the label. January 24 — JROH, PGM, RSA, UCR updated 1. PGM PGM provided the first update in several years. A new loading script was written for PGM to bring the data up to current standards. 2. YM Geocoordinates for YM have been appearing as integer degrees and have been highly inaccurate. This was a result of changes and updates to the refresh script for CCH. The loading script for YM has been updated and the geocoordinate problem has been fixed. 3. CSUSB, CLARK, IRVC, LA, MACF, PASA, SACT, UCSB, VVC These participants still have older, out-of-date datasets that are potentially being converted incorrectly when CCH is refreshed. IRVC has a number of poorly converted coordinates, specifically that are a source of yellow flags. These are next on the list for loading script updating. 4. Baja Specimens with 'Unknown' Municipalities Since May of 2016, it has been impossible to tell the difference between Baja California records and California records when the county/municipality field is "unknown".
1059805 Records with decimal Lat/Long, processed from coordinates on the label. 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. 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. 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. 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. 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: 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 file. 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 file. 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 file. 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.
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