xBio:D Wiki - User contributions [en]

User:Zjlahey

2018-10-03T18:31:33Z

Nfj: Creating user page for new user.

I am interested in the evolution and systematics of parasitoid Hymenoptera, particularly platygastroids and chalcidoids that attack sternorrhynchous Hemiptera (mainly whiteflies). Currently pursuing a PhD in the Department of Evolution, Ecology, and Organismal Biology at The Ohio State University under the tutelage of the coolest person ever, Dr. Norman Johnson.

User talk:Zjlahey

2018-10-03T18:31:33Z

Nfj: Welcome!

'''Welcome to ''xBio:D Wiki''!'''
We hope you will contribute much and well.
You will probably want to read the [[Help:Contents|help pages]].
Again, welcome and have fun! [[User:Nfj|Nfj]] ([[User talk:Nfj|talk]]) 14:31, 3 October 2018 (EDT)

User:Ix

2018-10-03T18:31:14Z

Nfj: Creating user page for new user.

Bio Museum Developer doing Bio Museum Developer Things

Lorem ipsum dolor sit amet, consectetur adipiscing elit. Maecenas sit amet ornare ipsum. Sed nec lectus sit amet diam posuere auctor in nec diam. Vivamus blandit egestas urna nec sollicitudin. Maecenas vitae egestas tortor. Mauris non tortor sit amet orci volutpat tempus. Sed malesuada est elit, laoreet porttitor dolor lobortis.

User talk:Ix

2018-10-03T18:31:14Z

Nfj: Welcome!

Data Entry Assistant (DEA) Help

2018-10-03T18:29:10Z

Nfj:

'''Introduction'''

This section contains information on preparing occurrence data for entry into the xBio:D database using a web application named [http://osuc.osu.edu/DEA2 Data Entry Assistant (DEA) 2.0]. Although this document was created for use in the previous version of DEA, many of the procedures and terminology remains the same. This guide includes instructions for formatting specimen records as well as references to facilitate taxonomic name recognition, locality georeferencing, etc.

== General Help ==
* [[Data Transcription Procedures]]
* [[Data Entry Template Information]]
* [[Data Entry Assistant (DEA) 2.0 Procedures]]
* [[Locality Georeferencing and Generation]]
* [[xBio:D Controlled Vocabularies]]

== References ==
* [[Taxonomic Name / Identification Recognition Reference]]
* [[Taxonomic Resources / Catalogs]]
* [[Geographic Resources / Gazetteers]]
* [[State / Province Codes for Countries]]

== Resources ==
* Specimen Data Template: [[File:Data_Entry_Template_31-Oct-2014.xls]]
* Pub-Cited Unvouchered Specimen Data Template: [[File:Data Entry Unv Template 04-Nov-2011.xls]]
* Pre-formatted Data Entry Template: [[File:DEA_data_entry_template-full 31-Oct-2014.xls]]
* Specimen Data Database Lookup: [[File:CUID_Lookup_01-Aug-2014.xlsm]]
* Political Divisions of Countries: [http://www.statoids.com Statoids]

[[Category:Data Entry Assistant]]

Data Entry Assistant (DEA) Help

2018-10-03T18:28:37Z

Nfj:

'''Introduction'''

This section contains information on preparing occurrence data for entry into the xBio:D database using a web application named [http://osuc.osu.edu/DEA2 Data Entry Assistant (DEA) 2.0]. Although this document was created for use in the previous version of DEA, much of the procedures and terminology remains the same. This guide includes instructions for formatting specimen records as well as references to facilitate taxonomic name recognition, locality georeferencing, etc.

== General Help ==
* [[Data Transcription Procedures]]
* [[Data Entry Template Information]]
* [[Data Entry Assistant (DEA) 2.0 Procedures]]
* [[Locality Georeferencing and Generation]]
* [[xBio:D Controlled Vocabularies]]

== References ==
* [[Taxonomic Name / Identification Recognition Reference]]
* [[Taxonomic Resources / Catalogs]]
* [[Geographic Resources / Gazetteers]]
* [[State / Province Codes for Countries]]

== Resources ==
* Specimen Data Template: [[File:Data_Entry_Template_31-Oct-2014.xls]]
* Pub-Cited Unvouchered Specimen Data Template: [[File:Data Entry Unv Template 04-Nov-2011.xls]]
* Pre-formatted Data Entry Template: [[File:DEA_data_entry_template-full 31-Oct-2014.xls]]
* Specimen Data Database Lookup: [[File:CUID_Lookup_01-Aug-2014.xlsm]]
* Political Divisions of Countries: [http://www.statoids.com Statoids]

[[Category:Data Entry Assistant]]

XBio:D Roadmap

2018-10-03T14:02:47Z

Nfj:

== The Database ==

The core of the database is information found on the specimen labels: this includes place of collection, time of collection, who did the collecting, how the specimens were collected, the identification of the specimen. This is all linked together using the unique identifier for each specimen (the collecting unit ID). This ID then links to any information on where the specimen is deposited and any images (or other media) of the specimen. The database also stores information on the published literature.

== IPT ==

The data in the database are publically available through our own portals. Additionally, the data are supposed to be regularly harvested and cached by data aggregators. These include the Global Biodiversity Information Facility ([http://www.gbif.org GBIF]), iDigBio ([http://www.example.com iDigBio]), and the SCAN network ([http://scan-bugs.org SCAN]). These aggregators do this by connecting to resources made available with the Integrated Publishing Toolkit (IPT), a Java program produced by GBIF. The scheme is that the database, at regular weekly intervals, produces a Darwin Core (DwC) file that contains the information we are sharing. Each resource we make available has a separate DwC file. We have, or intend to have anyway, a couple dozen such resources.

== Specimage ==

First, this app is intended to be pronounced "spess-ee-maj", a mashup of the words "specimen" and "image." Fundamentally, this is simply an image management system. It differs from similar commercially available programs in that the specimen seen in each image is linked to its collecting unit ID. This ID then provides access to all of the information in the core database that is associated with that specimen. Specimage also has an upload function to add new images. During that process a thumbnail and a web-friendly JPG version of the original image are produced, and the user specifies the license under which the image may be distributed. The core database contains only pointers to the location of the actual images.

== HOL ==

HOL - Hymenoptera On Line - is intended as a generic portal to the data we have. Text entered into the search box is interpreted in as many ways as possible: as a specimen ID, as the name of an organism, as a place name, as a person's name, etc. The results from these various options are presented as a series of tabs. Within each tab are expandable sections for predefined categories of information. Wildcards are accepted (% and _) as text input. Most of the information is live, i.e., directly extracted from the database and therefore as current as possible. Some summary information, however, is collated weekly and so may be slightly out-of-date. HOL also takes the lat/long coordinates for the places where specimens have been collected and uses GoogleMaps libraries to produce a map of those localities.

== OJ_Break API ==

OJ_Break is the name of the API used to interact with many (ultimately all!) of the web-based data portals. The output of OJ_Break are JSON objects that can then be parsed and formatted for display by Javascript code in the webpage.

== bioguid.osu.edu ==

The Biodiversity Informatics Standards group ([http://www.tdwg.org TDWG]) has set up and maintains (???) a vocabulary for the basic kinds of information that we share. In some of the data portals (e.g., HNS) we have the option of delivering the information in RDF. The domain bioguid.osu.edu is intended as a resolution mechanism for the (hopefully) globally unique identifiers that we support. In its original formulation TDWG recommend the use of life sciences identifiers (LSIDs) as the format for these identifiers. The community has now generally abandoned that format, and instead opted for stable URLs. The resolver software should be able to handle both formats. Unfortunately, bioguid.osu.edu presently seems to be offline.

== HNS ==

HNS is the Hymenoptera Name Server ([http://hns.osu.edu HNS]). Its function is to provide basic information associated with a taxonomic name. The code for this portal is actually compiled and stored within the database itself. It does not make use of the OJ_Break API.

== osuc-mgr ==

The osuc-mgr (database manager) is a set of forms used to enter or edit information within the database. It is protected by a username/password combination, and roles for different users are specified. It uses the OJ_Break API. This app is designed for entering/editing individual pieces of information. For batch input of specimen information see the description of DEA below. Information in the database may be edited in osuc-mgr, but not deleted outright.

== DEA ==

DEA, the Digital Entry Assistant ([http://dea.osu.edu DEA]), is intended as a means of batch upload of specimen collecting data. Users first transcribe specimen data into an Excel spreadsheet (template provided). Each row in the spreadsheet is a different specimen, and the columns are the attributes to be associated with the specimen. This spreadsheet is then used as the input to DEA. DEA is a set of Python scripts written in Django framework. Internally, a mySQL database stores information about data set uploads, status, etc. DEA takes the input, parses it, and then checks to see if the individual pieces of attribute data (such as the country in which a specimen was collected) are already in the database. If not, then the user is prompted to enter those missing pieces (via osuc-mgr). When all instances of missing data are resolved, DEA then manages the upload and proper storage of all of the information.

== vSysLab ==

vSysLab is the <u>v</u>irtual <u>S</u>ystematics <u>L</u>aboratory. At its core it stores information within the database to produce a matrix of species (the rows of the matrix) and their characteristics or attributes (the columns of the matrix). The key feature that distinguishes it from similar programs is that the names of the species provide links to the other information in the database, such as all the specimens with that name and all of the places that those specimens have been collected. vSysLab allows the user to link the textual descriptions of the atributes to images (via Specimage). It provides tools to manage species and characters, as well as a variety of modes of formatting the output.

== Literature Library ==

We are shifting from maintaining a hard-copy library of publications, to one of PDFs only. We currently have over 10,000 publications in the library. The database stores pointers to the actual storage location of the PDFs. PDFs are uploaded through an osuc-mgr form.

== Hardware Layout ==

With our ongoing shift to a virtual environment, most of this description is obsolete. However, it may help to understand the original crosstalk between computers. We eventually ended up with 3 computers running the system, one running Linux (128.146.250.24), an old Windows desktop (128.146.250.117), and a newer Windows Server (128.146.250.252). These had multiple domain names associated with them, just to help make it all more confusing:

252:
<ul>
<li> osuc.osu.edu: Collection's web server
<li> specimage.osu.edu: Specimage, both the code as well as the images themselves
<li> wasps.osu.edu: Johnson lab web server
<li> osuc.osu.edu/DEA2: DEA
</ul>

24:
<ul>
<li> osuc.biosci.ohio-state.edu: the Oracle database
<li> osuc-mgr.osu.edu: the osuc-mgr set of forms
<li> hns.osu.edu: Hymenoptera Name Server (HNS)
<li> hol.osu.edu: Hymenoptera On Line (HOL)
<li> vsyslab.osu.edu: vSysLab
<li> bioguid.osu.edu: Globally unique identifer resolving service (not absolutely sure that it was here. We need to find and restore it!)
</ul>

117:
<ul>
<li> hymfiles.biosci.ohio-state.edu: PDF libraries
<li> xbiod.osu.edu: IPT (in ./ipt), xBio:D wiki (in ./xbiodWiki)
</ul>

I don't see any communication going <u>from</u> 117 to 24. However, all other combinations seem to be there: 24 -> 252, 24 -> 117, and 252 -> 24.

XBio:D Roadmap

2018-10-03T13:52:47Z

Nfj:

== The Database ==

The core of the database is information found on the specimen labels: this includes place of collection, time of collection, who did the collecting, how the specimens were collected, the identification of the specimen. This is all linked together using the unique identifier for each specimen (the collecting unit ID). This ID then links to any information on where the specimen is deposited and any images (or other media) of the specimen. The database also stores information on the published literature.

== IPT ==

The data in the database are publically available through our own portals. Additionally, the data are supposed to be regularly harvested and cached by data aggregators. These include the Global Biodiversity Information Facility ([http://www.gbif.org GBIF]), iDigBio ([http://www.example.com iDigBio]), and the SCAN network ([http://scan-bugs.org SCAN]). These aggregators do this by connecting to resources made available with the Integrated Publishing Toolkit (IPT), a Java program produced by GBIF. The scheme is that the database, at regular weekly intervals, produces a Darwin Core (DwC) file that contains the information we are sharing. Each resource we make available has a separate DwC file. We have, or intend to have anyway, a couple dozen such resources.

== Specimage ==

First, this app is intended to be pronounced "spess-ee-maj", a mashup of the words "specimen" and "image." Fundamentally, this is simply an image management system. It differs from similar commercially available programs in that the specimen seen in each image is linked to its collecting unit ID. This ID then provides access to all of the information in the core database that is associated with that specimen. Specimage also has an upload function to add new images. During that process a thumbnail and a web-friendly JPG version of the original image are produced, and the user specifies the license under which the image may be distributed. The core database contains only pointers to the location of the actual images.

== HOL ==

HOL - Hymenoptera On Line - is intended as a generic portal to the data we have. Text entered into the search box is interpreted in as many ways as possible: as a specimen ID, as the name of an organism, as a place name, as a person's name, etc. The results from these various options are presented as a series of tabs. Within each tab are expandable sections for predefined categories of information. Wildcards are accepted (% and _) as text input. Most of the information is live, i.e., directly extracted from the database and therefore as current as possible. Some summary information, however, is collated weekly and so may be slightly out-of-date. HOL also takes the lat/long coordinates for the places where specimens have been collected and uses GoogleMaps libraries to produce a map of those localities.

== OJ_Break API ==

OJ_Break is the name of the API used to interact with many (ultimately all!) of the web-based data portals. The output of OJ_Break are JSON objects that can then be parsed and formatted for display by Javascript code in the webpage.

== bioguid.osu.edu ==

The Biodiversity Informatics Standards group ([http://www.tdwg.org TDWG]) has set up and maintains (???) a vocabulary for the basic kinds of information that we share. In some of the data portals (e.g., HNS) we have the option of delivering the information in RDF. The domain bioguid.osu.edu is intended as a resolution mechanism for the (hopefully) globally unique identifiers that we support. In its original formulation TDWG recommend the use of life sciences identifiers (LSIDs) as the format for these identifiers. The community has now generally abandoned that format, and instead opted for stable URLs. The resolver software should be able to handle both formats. Unfortunately, bioguid.osu.edu presently seems to be offline.

== HNS ==

HNS is the Hymenoptera Name Server ([http://hns.osu.edu HNS]). Its function is to provide basic information associated with a taxonomic name. The code for this portal is actually compiled and stored within the database itself. It does not make use of the OJ_Break API.

== osuc-mgr ==

The osuc-mgr (database manager) is a set of forms used to enter or edit information within the database. It is protected by a username/password combination, and roles for different users are specified. It uses the OJ_Break API. This app is designed for entering/editing individual pieces of information. For batch input of specimen information see the description of DEA below. Information in the database may be edited in osuc-mgr, but not deleted outright.

== DEA ==

DEA, the Digital Entry Assistant ([http://dea.osu.edu DEA]), is intended as a means of batch upload of specimen collecting data. Users first transcribe specimen data into an Excel spreadsheet (template provided). Each row in the spreadsheet is a different specimen, and the columns are the attributes to be associated with the specimen. This spreadsheet is then used as the input to DEA. DEA is a set of Python scripts written in Django framework. Internally, a mySQL database stores information about data set uploads, status, etc. DEA takes the input, parses it, and then checks to see if the individual pieces of attribute data (such as the country in which a specimen was collected) are already in the database. If not, then the user is prompted to enter those missing pieces (via osuc-mgr). When all instances of missing data are resolved, DEA then manages the upload and proper storage of all of the information.

== vSysLab ==

vSysLab is the <u>v</u>irtual <u>S</u>ystematics <u>L</u>aboratory. At its core it stores information within the database to produce a matrix of species (the rows of the matrix) and their characteristics or attributes (the columns of the matrix). The key feature that distinguishes it from similar programs is that the names of the species provide links to the other information in the database, such as all the specimens with that name and all of the places that those specimens have been collected. vSysLab allows the user to link the textual descriptions of the atributes to images (via Specimage). It provides tools to manage species and characters, as well as a variety of modes of formatting the output.

== Literature Library ==

We are shifting from maintaining a hard-copy library of publications, to one of PDFs only. We currently have over 10,000 publications in the library. The database stores pointers to the actual storage location of the PDFs. PDFs are uploaded through an osuc-mgr form.

== Hardware Layout ==

With our ongoing shift to a virtual environment, most of this description is obsolete. However, it may help to understand the original crosstalk between computers. We eventually ended up with 3 computers running the system, one running Linux (128.146.250.24), an old Windows desktop (128.146.250.117), and a newer Windows Server (128.146.250.252). These had multiple domain names associated with them, just to help make it all more confusing:

252:
<ul>
<li> osuc.osu.edu: Collection's web server
<li> specimage.osu.edu: Specimage
<li> wasps.osu.edu: Johnson lab web server
</ul>

24:
<ul>
<li> osuc.biosci.ohio-state.edu: the Oracle database
<li> osuc-mgr.osu.edu: the osuc-mgr set of forms
<li> hns.osu.edu: Hymenoptera Name Server (HNS)
<li> hol.osu.edu: Hymenoptera On Line (HOL)
<li> vsyslab.osu.edu: vSysLab
</ul>

117:
<ul>
<li> hymfiles.biosci.ohio-state.edu: PDF libraries
<li> : IPT
</ul>

XBio:D Roadmap

2018-10-03T13:21:06Z

Nfj:

XBio:D Roadmap

2018-10-03T12:56:14Z

Nfj:

XBio:D Roadmap

2018-10-03T12:47:21Z

Nfj: Created page with " == The Database == The core of the database is information found on the specimen labels: this includes place of collection, time of collection, who did the collecting, how t..."

Main Page

2018-10-03T12:14:38Z

Nfj:

'''Welcome to the xBio:D Help Wiki at the Ohio State University'''

This wiki is a semi-protected wiki with only verified users able to manipulate the contents. If you are a user and would like to become verified, contact [mailto:hol-help@osu.edu hol-help@osu.edu] and request a change in status. Please contribute any additional knowledge to the wiki pages to ensure a more greatly informed base of users.

== Insect Collection (OSUC) Protocols (internal use only) ==
* [[Sorting Platygastroidea Identified Material]]
* [[Hymenoptera Cataloging Workflow]]
* [[Annotating Publications]]
* [[Extended-Focus Imaging Using Auto-Montage System]]

== Insect Collection (OSUC) Cyberinfrastructure Management Private Portal ==
* [[Collection (OSUC) Private Portal]]

== xBio:D Web Services Help ==
=== Applications ===
* [[Data Entry Assistant (DEA) Help]]
* [[vSysLab Help]]
* [[Database Manager Help]]
* [[Specimage Help]]
* [[Hymenoptera Online (HOL) Help]]

=== APIs ===
* [[xBio:D Javascript Library Reference]]
* [[OJ_Break API Reference]]
* [[OJ_Break Version 2 API Reference]]

=== Collaborators ===
* [[xBio:D Occurrence Collaborators]]
* [[xBio:D Taxonomic Collaborators]]
* [[xBio:D Literature Collaborators]]
* [[xBio:D Media Collaborators]]

== Fish Collection (OSUM) Protocols ==
* [[Data Entry Procedures]]

== Ohio Biodiversity Conservation Partnership (OBCP) Informatics Portal ==
* [[OBCP Informatics Portal]]

== Trissolcus / Stinkbug Information Portal ==
* [[Trissolcus / Stinkbug Procedures]]

== Current System Status - Loosely Updated ==
* [[Museum Status]]

== xBio:D Roadmap ==
* [[xBio:D Roadmap]]

OJ Break Version 2 API Reference

2018-07-09T14:59:35Z

Nfj: Updated the url to now point to the new server

OJ Break API Reference

2018-07-09T14:57:34Z

Nfj: Updated the page to point to the new api urls.

'''Introduction'''

OJ_Break is the name of the xBio:D RESTful API service to facilitate discovery of data within the xBio:D database. The API can respond with JavaScript Object Notation (JSON), XML, or JSON with padding (JSONP) and accepts HTTP GET and POST requests indiscriminately. The backend of the API is written in Oracle's PL/SQL database language, which is fast but often inflexible, while a Python presentation layer mitigates request handling and authentication.

The reference for version 2 of the API can be found here: [[OJ_Break_Version_2_API_Reference]]

== API Information and Access ==
This page specifies the methods and data defined by OJ_Break Version 1. Using the OJ_Break Version 1 API requires calling methods with corresponding, method specific parameters (found in this page) and a few other required parameters. These include specifying a return ''format'' and an API access ''key''.

Example: https://osuc.biosci.ohio-state.edu/cgi-bin/OJ_Break_API.py/getTaxonStats?tnuid=30148&format=json&key=FBF57A9F7A666FC0E0430100007F0CDC

To read more about using the OJ_Break Version 1 API, go to [[OJ_Break API Access]].

== Procedural Reference ==
=== Agent ===
==== getCollectorInfo ====
===== Description =====
===== Parameters =====
* ''collector_id'': number
* ''format'': string
* ''key'': string
===== Return =====
* ''collector_info'': array of author_info

===== Example =====
https://osuc.biosci.ohio-state.edu/cgi-bin/OJ_Break_API.py/getCollectorInfo?collector_id=2&format=json&key=FBF57A9F7A666FC0E0430100007F0CDC

==== getAuthorPubs ====
===== Description =====
===== Parameters =====
* ''author_id'': number
* ''format'': string
* ''key'': string
===== Return =====
* ''pubs'': array of literature_extended

===== Example =====
https://osuc.biosci.ohio-state.edu/cgi-bin/OJ_Break_API.py/getAuthorPubs?author_id=2&format=json&key=FBF57A9F7A666FC0E0430100007F0CDC

==== getCollTrips2 ====
===== Description =====
===== Parameters =====
* ''collector_id'': number
* ''format'': string
* ''key'': string
===== Return =====
* ''coll_trips'': array of collection_basic, taxon_basic, loc_coords, and collector.

===== Example =====
https://osuc.biosci.ohio-state.edu/cgi-bin/OJ_Break_API.py/getCollTrips2?collector_id=2&format=json&key=FBF57A9F7A666FC0E0430100007F0CDC

==== getAuthorTaxa ====
===== Description =====
===== Parameters =====
* ''author_id'': number
* ''format'': string
* ''key'': string

===== Return =====
''taxa'': array of taxon_basic

===== Example =====
https://osuc.biosci.ohio-state.edu/cgi-bin/OJ_Break_API.py/getAuthorTaxa?author_id=2&format=json&key=FBF57A9F7A666FC0E0430100007F0CDC

=== Taxon ===
==== getTaxonStats ====
===== Description =====
Get some basic taxonomic statistics for a taxon from a tnuid.
===== Parameters =====
* ''tnuid'': number
* ''format'': string
* ''key'': string
===== Return =====
* ''taxon'': string
* ''author'': string
* ''stats'': taxon_stats

===== Example =====
https://osuc.biosci.ohio-state.edu/cgi-bin/OJ_Break_API.py/getTaxonStats?tnuid=30148&format=json&key=FBF57A9F7A666FC0E0430100007F0CDC

==== getTaxonInfo ====
===== Description =====
Get some basic taxonomic information for a taxon from a tnuid.
===== Parameters =====
* ''tnuid'': number
* ''inst_id'': number
* ''format'': string
* ''key'': string
===== Return =====
* ''taxon_rel_extended'' class with below extensions
* ''valid_taxon'': taxon_basic (only present when defined)
* ''parent_taxon'': taxon_basic
* ''hier'': taxon_hierarchy
* ''source'': taxon_source
* ''common_names'': array of common_name
* ''orig_desc'': contrib_literature_basic (only present when defined)
* ''stats'': taxon_info_stats
* ''contribs'': array of contribution
===== Example =====
https://osuc.biosci.ohio-state.edu/cgi-bin/OJ_Break_API.py/getTaxonInfo?tnuid=30148&inst_id=0&format=json&key=FBF57A9F7A666FC0E0430100007F0CDC

==== getTaxonHierarchy ====
===== Description =====
Get the taxonomic hierarachy in which a taxon is at the terminal node from a tnuid.
===== Parameters =====
* ''tnuid'': number
* ''format'': string
* ''key'': string
===== Return =====
* ''taxon'': string
* ''author'': string
* ''hier'': taxon_hierarchy
===== Example =====
https://osuc.biosci.ohio-state.edu/cgi-bin/OJ_Break_API.py/getTaxonHierarchy?tnuid=30148&format=json&key=FBF57A9F7A666FC0E0430100007F0CDC

==== getIncludedTaxa ====
===== Description =====
Get the taxa that are directly included within a taxon but not synonymous with it.
===== Parameters =====
* ''tnuid'': number
* ''inst_id'': number
* ''showSyns'': boolean_flag
* ''showFossils'': boolean_flag
* ''types_only'': boolean_flag
* ''show_num_spms'': boolean_flag
* ''format'': string
* ''key'': string

===== Return =====
* ''tnuid'': number
* ''parent_tnuid'': number
* ''includedTaxa'': array of taxon_extended
===== Example =====
https://osuc.biosci.ohio-state.edu/cgi-bin/OJ_Break_API.py/getIncludedTaxa?tnuid=491&inst_id=0&showSyns=Y&showFossils=Y&types_only=N&show_num_spms=N&format=json&key=FBF57A9F7A666FC0E0430100007F0CDC

==== getTaxonSynonyms ====
===== Description =====
Get the taxa that are objectively or subjectively synonymous with a taxon.
===== Parameters =====
* ''tnuid'': number
* ''showFossils'': boolean_flag
* ''format'': string
* ''key'': string

===== Return =====
* ''synonyms'': array of taxon_rel_extended
===== Example =====
https://osuc.biosci.ohio-state.edu/cgi-bin/OJ_Break_API.py/getTaxonSynonyms?tnuid=30148&showFossils=Y&format=json&key=FBF57A9F7A666FC0E0430100007F0CDC

==== getLocalities ====
===== Description =====
Get the localities from vouchered and unvouchered records for a taxon.
===== Parameters =====
* ''tnuid'': number
* ''inst_id'': number
* ''precDecimals'': number
* ''showChildren'': boolean_flag
* ''format'': string
* ''key'': string

===== Return =====
* ''localities'': array of loc_coords
===== Example =====
https://osuc.biosci.ohio-state.edu/cgi-bin/OJ_Break_API.py/getLocalities?tnuid=30148&inst_id=0&precDecimals=4&showChildren=Y&format=json&key=FBF57A9F7A666FC0E0430100007F0CDC

==== getLocalities ====
===== Description =====
Get the localities within geopolitical divisions from vouchered and unvouchered records for a taxon.
===== Parameters =====
* ''tnuid'': number
* ''pnids'': array of pnid
* ''inst_id'': number
* ''precDecimals'': number
* ''showChildren'': boolean_flag
* ''format'': string
* ''key'': string

===== Return =====
* ''localities'': array of loc_coords
===== Example =====
https://osuc.biosci.ohio-state.edu/cgi-bin/OJ_Break_API.py/getLocalities?tnuid=30148&pnids=5816,5735&inst_id=0&precDecimals=4&showChildren=Y&format=json&key=FBF57A9F7A666FC0E0430100007F0CDC

==== getCuids ====
===== Description =====
Get the occurrence identifiers (collecting unit IDs) for a taxon.
===== Parameters =====
* ''tnuid'': number
* ''showChildren'': boolean_flag
* ''inst_id'': number
* ''pnids'': array of pnid
* ''format'': string
* ''key'': string

===== Return =====
* ''cuids'': array of cuid
===== Example =====
https://osuc.biosci.ohio-state.edu/cgi-bin/OJ_Break_API.py/getCuids?tnuid=30148&showChildren=Y&inst_id=1&pnids=&format=json&key=FBF57A9F7A666FC0E0430100007F0CDC

==== getCuids ====
===== Description =====
Get the occurrence identifiers (collecting unit IDs) for selected taxa.
===== Parameters =====
* ''tnuids'': array of tnuid
* ''pnids'': array of pnid
* ''format'': string
* ''key'': string

===== Return =====
* ''cuids'': array of cuid
===== Example =====
https://osuc.biosci.ohio-state.edu/cgi-bin/OJ_Break_API.py/getCuids?tnuids=30148,491&pnids=5816,5735&format=json&key=FBF57A9F7A666FC0E0430100007F0CDC

==== getTypes ====
===== Description =====
Gets information and specimen types for a specified taxon.

===== Parameters =====
* ''tnuid'': number
* ''showSyns'': boolean_flag
* ''inst_id'': number
* ''primary_only'': boolean_flag
* ''taxon_author_search'': string
* ''offset'': number
* ''limit'': number
* ''format'': string
* ''key'': string

===== Return =====
* ''num_records'': number
* ''types'': array of type_extended

===== Example =====
https://osuc.biosci.ohio-state.edu/cgi-bin/OJ_Break_API.py/getTypes?tnuid=434&showSyns=F&inst_id=1&primary_only=Y&taxon_author_search=&offset=1&limit=10&format=json&key=FBF57A9F7A666FC0E0430100007F0CDC

==== getInsts ====
===== Description =====
Gets institutions which hold specimens for a selected taxon.

===== Parameters =====
* ''tnuid'': number
* ''format'': string
* ''key'': string

===== Return =====
* ''collections'': array of collection_extended

===== Example =====
https://osuc.biosci.ohio-state.edu/cgi-bin/OJ_Break_API.py/getInsts?tnuid=30148&format=json&key=FBF57A9F7A666FC0E0430100007F0CDC

==== getTaxonLiterature (deprecated) ====
===== Description =====
Deprecated. Use getTaxonLit instead
===== Parameters =====
* ''tnuid'': number
* ''showSyns'': string
* ''format'': string
* ''key'': string

===== Return =====
* ''lit'': pubs
===== Example =====
https://osuc.biosci.ohio-state.edu/cgi-bin/OJ_Break_API.py/getTaxonLiterature?tnuid=30148&showSyns=Y&format=json&key=FBF57A9F7A666FC0E0430100007F0CDC

==== getTaxonLit ====
===== Description =====
Preferred. Get literature for a selected taxon.
===== Parameters =====
* ''tnuid'': number
* ''showSyns'': boolean_flag
* ''format'': string
* ''key'': string

===== Return =====
* ''pubs'': array of pub_extended

===== Example =====
https://osuc.biosci.ohio-state.edu/cgi-bin/OJ_Break_API.py/getTaxonLit?tnuid=30148&showSyns=Y&format=json&key=FBF57A9F7A666FC0E0430100007F0CDC

==== getAssociations ====
===== Description =====
Get evolutionary relationships for a certain taxon.
===== Parameters =====
* ''tnuid'': number
* ''rank_grouping'': string
* ''format'': string
* ''key'': string

===== Return =====
* ''associations'': array of association

===== Example =====
https://osuc.biosci.ohio-state.edu/cgi-bin/OJ_Break_API.py/getAssociations?tnuid=491&rank_grouping=&format=json&key=FBF57A9F7A666FC0E0430100007F0CDC

==== getHabitats ====
===== Description =====
Get descriptions of the habitats that a selected specimen inhabits.

===== Parameters =====
* ''tnuid'': number
* ''format'': string
* ''key'': string

===== Return =====
* ''habitats'': array of habitat

===== Example =====
https://osuc.biosci.ohio-state.edu/cgi-bin/OJ_Break_API.py/getHabitats?tnuid=30148&format=json&key=FBF57A9F7A666FC0E0430100007F0CDC

==== getTaxonMedia ====
===== Description =====
Get images, videos, or sound clips of a selected taxon.
===== Parameters =====
* ''tnuid'': number
* ''format'': string
* ''key'': string

===== Return =====
* ''media'': array of media_basic

===== Example =====
https://osuc.biosci.ohio-state.edu/cgi-bin/OJ_Break_API.py/getTaxonMedia?tnuid=30148&format=json&key=FBF57A9F7A666FC0E0430100007F0CDC

==== getTaxonBreakdown ====
===== Description =====
Get count of genders and total specimen included in the current rank.
===== Parameters =====
* ''tnuid'': number
* ''format'': string
* ''key'': string

===== Return =====
* ''taxa'': array of taxon_basic with below extension
** ''count'': number
* ''sex'': array of spm_sex

===== Example =====
https://osuc.biosci.ohio-state.edu/cgi-bin/OJ_Break_API.py/getTaxonBreakdown?tnuid=491&format=json&key=FBF57A9F7A666FC0E0430100007F0CDC

==== getTaxonPhenology ====
===== Description =====
Get taxon specimens by date.
===== Parameters =====
* ''tnuid'': number
* ''format'': string
* ''key'': string

===== Return =====
* ''spms'': array of below elements
** ''date'': string
** ''sort_date'': string
** ''cuid'': string

===== Example =====
https://osuc.biosci.ohio-state.edu/cgi-bin/OJ_Break_API.py/getTaxonPhenology?tnuid=30148&format=json&key=FBF57A9F7A666FC0E0430100007F0CDC

==== getTaxonNewTaxaByPub ====
===== Description =====
Get count of new specimens for a specific taxon by publication.
===== Parameters =====
* ''tnuid'': number
* ''validOnly'': boolean_flag
* ''format'': string
* ''key'': string

===== Return =====
* ''pubs'': array of literature_extended with below extension
** ''taxa_num'': string

===== Example =====
https://osuc.biosci.ohio-state.edu/cgi-bin/OJ_Break_API.py/getTaxonNewTaxaByPub?tnuid=491&validOnly=Y&format=json&key=FBF57A9F7A666FC0E0430100007F0CDC

==== getTaxonNewTaxaByYear ====
===== Description =====
Get count of new specimens for a specific taxon by year.
===== Parameters =====
* ''tnuid'': number
* ''validOnly'': string
* ''format'': string
* ''key'': string

===== Return =====
* ''years'': array of below elements
** ''taxa_num'': string
** ''year'': string

===== Example =====
https://osuc.biosci.ohio-state.edu/cgi-bin/OJ_Break_API.py/getTaxonNewTaxaByYear?tnuid=52&validOnly=Y&format=json&key=FBF57A9F7A666FC0E0430100007F0CDC

==== getTaxonStatsForYear ====
===== Description =====
Get stats, such as image count, new genera introduced, new specimen introduced, and more by year for a selected taxon.
===== Parameters =====
* ''tnuid'': number
* ''stats_year'': number
* ''format'': string
* ''key'': string

===== Return =====
* ''stats'': array of below elements
** ''new_spm_num'': number
** ''all_spm_num'': number
** ''new_taxa_spm_num'': array of number
** ''all_taxa_spm_num'': array of number
** ''new_images_num'': number
** ''all_images_num'': number
** ''spm_years'': array of string
** ''images_years'': array of string

===== Example =====
https://osuc.biosci.ohio-state.edu/cgi-bin/OJ_Break_API.py/getTaxonStatsForYear?tnuid=30148&stats_year=2014&format=json&key=FBF57A9F7A666FC0E0430100007F0CDC

=== Occurrence ===
==== Specimen Record ====
===== getSpmInfo =====
====== Description ======
Get info for a specific specimen occurrence.
====== Parameters ======
* ''cuid'': string
* ''format'': string
* ''key'': string

====== Return ======
* ''spmInfo'': record_vouchered
====== Example ======
https://osuc.biosci.ohio-state.edu/cgi-bin/OJ_Break_API.py/getSpmInfo?cuid=OSUC+59557&format=json&key=FBF57A9F7A666FC0E0430100007F0CDC

===== getSpmsInfo =====
====== Description ======
Get info for multiple specimen occurrences.
====== Parameters ======
* ''cuids'': array of string
* ''format'': string
* ''key'': string

====== Return ======
* ''spmsInfo'': array of record_vouchered
====== Example ======
https://osuc.biosci.ohio-state.edu/cgi-bin/OJ_Break_API.py/getSpmsInfo?cuids=OSUC+59557,OSUC+56308&format=json&key=FBF57A9F7A666FC0E0430100007F0CDC

==== Unvouchered Record ====
===== getUnvoucheredRecord =====
====== Description ======
Get specimen record information for a selected unvouchered specimen.
====== Parameters ======
* ''unv_id'': number
* ''format'': string
* ''key'': string

====== Return ======
* ''unvoucheredRecord'': record_unvouchered

====== Example ======
https://osuc.biosci.ohio-state.edu/cgi-bin/OJ_Break_API.py/getUnvoucheredRecord?unv_id=1&format=json&key=FBF57A9F7A666FC0E0430100007F0CDC

===== getUnvoucheredRecords =====
====== Description ======
Get unvouchered specimen records for a selected taxon and place.
====== Parameters ======
* ''tnuid'': number
* ''showChildren'': string
* ''pnids'': array of number
* ''format'': string
* ''key'': string

====== Return ======
* ''unvoucheredRecords'': array of record_unvouchered

====== Example ======
https://osuc.biosci.ohio-state.edu/cgi-bin/OJ_Break_API.py/getUnvoucheredRecords?tnuid=44&showChildren=Y&pnids=&format=json&key=FBF57A9F7A666FC0E0430100007F0CDC

=== Locality ===
==== getLocalityInfo ====
===== Description =====
Get basic information for a specific locality, including specimen occurrences, place hierarchy, and coordinates.
===== Parameters =====
* ''loc_id'': number
* ''tnuid'': number
* ''inst_id'': number
* ''per_id'': number
* ''pnid'': number
* ''showChildren'': string
* ''completeSpmInfo'': string
* ''format'': string
* ''key'': string

===== Return =====
* ''locInfo'': array of loc_info with below extensions
** ''hier'': array of place
** ''cuids'': array of record_vouchered (only present if specified) or array of cuid
** ''sex'': array of spm_sex

===== Example =====
https://osuc.biosci.ohio-state.edu/cgi-bin/OJ_Break_API.py/getLocalityInfo?loc_id=1&tnuid=30148&inst_id=1&per_id=1&pnid=1&showChildren=Y&completeSpmInfo=Y&format=json&key=FBF57A9F7A666FC0E0430100007F0CDC

==== getUnvLocalityInfo ====
===== Description =====
Get locality information and occurrences (specimens) for a selected locality. The request can be narrowed down further by selected multiple parameter options.
===== Parameters =====
* ''loc_id'': number
* ''tnuid'': number
* ''per_id'': number
* ''pnid'': number
* ''showChildren'': string
* ''format'': string
* ''key'': string

===== Return =====
* ''locInfo'': loc_info with below extensions
** ''hier'': array of place
** ''cuids'': array of cuid

===== Example =====
https://osuc.biosci.ohio-state.edu/cgi-bin/OJ_Break_API.py/getUnvLocalityInfo?loc_id=1&tnuid=30148&per_id=1&pnid=1&showChildren=Y&format=json&key=FBF57A9F7A666FC0E0430100007F0CDC

=== Place / Geopolitical Entity ===
==== getPlaceInfo ====
===== Description =====
Get basic place information including the place hierarchy, number of specimens, and number of species.
===== Parameters =====
* ''place_id'': number
* ''format'': string
* ''key'': string

===== Return =====
* ''place_info'': place with below extension
** ''hier'': array of place
** ''num_species'': number
** ''num_spms'': number

===== Example =====
https://osuc.biosci.ohio-state.edu/cgi-bin/OJ_Break_API.py/getPlaceInfo?place_id=1&format=json&key=FBF57A9F7A666FC0E0430100007F0CDC

==== getSubdivisions ====
===== Description =====
Get smaller levels of divisions for a selected place.
===== Parameters =====
* ''place_id'': number
* ''format'': string
* ''key'': string

===== Return =====
* ''subdivs'': array of place

===== Example =====
https://osuc.biosci.ohio-state.edu/cgi-bin/OJ_Break_API.py/getSubdivisions?place_id=1&format=json&key=FBF57A9F7A666FC0E0430100007F0CDC

==== getGeoTaxa ====
===== Description =====
Get taxonomic information from a specified place.

===== Parameters =====
* ''place_id'': number
* ''format'': string
* ''key'': string

===== Return =====
* ''taxa'': array of taxon_basic with below extensions
** ''valid_taxon'': taxon_basic (only present when defined)
** ''hier'': taxon_hierarchy
** ''count'': number
** ''rank'': string

===== Example =====
https://osuc.biosci.ohio-state.edu/cgi-bin/OJ_Break_API.py/getGeoTaxa?place_id=1&format=json&key=FBF57A9F7A666FC0E0430100007F0CDC

==== getGeoCollTrips ====
===== Description =====
Get collecting trips info for a specified place.
===== Parameters =====
* ''place_id'': number
* ''format'': string
* ''key'': string

===== Return =====
* ''coll_trips'': array of loc_basic and collector.

===== Example =====
https://osuc.biosci.ohio-state.edu/cgi-bin/OJ_Break_API.py/getGeoCollTrips?place_id=1&format=json&key=FBF57A9F7A666FC0E0430100007F0CDC

==== getGeoCollTrips2 ====
===== Description =====
Get collecting trips and taxa info for a specified place.

===== Parameters =====
* ''place_id'': number
* ''format'': string
* ''key'': string

===== Return =====
* ''coll_trips'': array of taxon_basic, collection, collector and loc_basic with below extension
** ''valid_taxon'': taxon_basic (only present when defined)

===== Example =====
https://osuc.biosci.ohio-state.edu/cgi-bin/OJ_Break_API.py/getGeoCollTrips2?place_id=1&format=json&key=FBF57A9F7A666FC0E0430100007F0CDC

==== getGeoInsts ====
===== Description =====
Get institutions from a selected place.
===== Parameters =====
* ''place_id'': number
* ''format'': string
* ''key'': string

===== Return =====
* ''collections'': array of collection_extended

===== Example =====
https://osuc.biosci.ohio-state.edu/cgi-bin/OJ_Break_API.py/getGeoInsts?place_id=1&format=json&key=FBF57A9F7A666FC0E0430100007F0CDC

=== Literature ===
==== getLitReference ====
===== Description =====
Get the reference for a selected publication.
===== Parameters =====
* ''pub_id'': number
* ''format'': string
* ''key'': string

===== Return =====
* ''pub_ref'': literature_extended

===== Example =====
https://osuc.biosci.ohio-state.edu/cgi-bin/OJ_Break_API.py/getLitReference?pub_id=419&format=json&key=FBF57A9F7A666FC0E0430100007F0CDC

==== getLitParts ====
===== Description =====
Get parts of the selected publication, such as pages, pdf urls, chapters, titles, authors, and more.
===== Parameters =====
* ''pub_id'': number
* ''format'': string
* ''key'': string

===== Return =====
* ''pub_parts'': array of literature_extended

===== Example =====
https://osuc.biosci.ohio-state.edu/cgi-bin/OJ_Break_API.py/getLitParts?pub_id=20239&format=json&key=FBF57A9F7A666FC0E0430100007F0CDC

==== getPubTaxonCitation ====
===== Description =====
Get cited taxon information from a selected publication.
===== Parameters =====
* ''pub_id'': number
* ''format'': string
* ''key'': string

===== Return =====
* ''pub_cits'': array of pub_basic and taxon_basic with below extensions
** ''tnucid'': number
** ''rank'': string
* ''public'': string
* ''author'': string

===== Example =====
https://osuc.biosci.ohio-state.edu/cgi-bin/OJ_Break_API.py/getPubTaxonCitation?pub_id=419&format=json&key=FBF57A9F7A666FC0E0430100007F0CDC

==== getPubAssocCitation ====
===== Description =====

===== Parameters =====
* ''pub_id'': number
* ''format'': string
* ''key'': string

===== Return =====
* ''assoc_cits'': array of ..
===== Example =====
https://osuc.biosci.ohio-state.edu/cgi-bin/OJ_Break_API.py/getPubAssocCitation?pub_id=23683&format=json&key=FBF57A9F7A666FC0E0430100007F0CDC

=== Journal ===
==== getJournalInfo ====
===== Description =====

===== Parameters =====
* ''jrnl_id'': number
* ''format'': string
* ''key'': string

===== Return =====
* ''journal_info'': array of below elements
** ''name'': string
** ''url'': string
** ''is_public'': string
** ''copyright_holder'': string
** ''num_articles'': number
** ''num_pdfs'': number
** ''num_taxa'': number
** ''last_article_time'': string

===== Example =====
https://osuc.biosci.ohio-state.edu/cgi-bin/OJ_Break_API.py/getJournalInfo?jrnl_id=1&format=json&key=FBF57A9F7A666FC0E0430100007F0CDC

==== getJournalPubs ====
===== Description =====

===== Parameters =====
* ''jrnl_id'': number
* ''format'': string
* ''key'': string

===== Return =====
* ''pubs'': array of literature_extended

===== Example =====
https://osuc.biosci.ohio-state.edu/cgi-bin/OJ_Break_API.py/getJournalPubs?jrnl_id=1&format=json&key=FBF57A9F7A666FC0E0430100007F0CDC

==== getJournalTaxa ====
===== Description =====

===== Parameters =====
* ''jrnl_id'': number
* ''format'': string
* ''key'': string

===== Return =====
* ''taxa'': array of taxon_basic
===== Example =====
https://osuc.biosci.ohio-state.edu/cgi-bin/OJ_Break_API.py/getJournalTaxa?jrnl_id=1&format=json&key=FBF57A9F7A666FC0E0430100007F0CDC

=== Institution ===
==== getCollectionInfo ====
===== Description =====

===== Parameters =====
* ''inst_id'': number
* ''format'': string
* ''key'': string

===== Return =====
* ''collection_info'': array of collection_extended with below extensions
** ''vouchered'': boolean
** ''num_prim_types'': number
** ''num_sec_types'': number
** ''num_species'': number
** ''last_spm_time'': string
** ''oldest_spm'': array of below elements
*** ''cuid'': string
*** ''coll_date'': string

===== Example =====
https://osuc.biosci.ohio-state.edu/cgi-bin/OJ_Break_API.py/getCollectionInfo?inst_id=21&format=json&key=FBF57A9F7A666FC0E0430100007F0CDC

==== getPrimaryTypes ====
===== Description =====
Get specimen of which the description of a new species is based.
===== Parameters =====
* ''inst_id'': number
* ''format'': string
* ''key'': string

===== Return =====
* ''types'': array of type

===== Example =====
https://osuc.biosci.ohio-state.edu/cgi-bin/OJ_Break_API.py/getPrimaryTypes?inst_id=6&format=json&key=FBF57A9F7A666FC0E0430100007F0CDC

==== getSecondaryTypes ====
===== Description =====
Get specimen that are occurrences of a specific species, but not a primary type.
===== Parameters =====
* ''inst_id'': number
* ''format'': string
* ''key'': string

===== Return =====
* ''types'': array of type

===== Example =====
https://osuc.biosci.ohio-state.edu/cgi-bin/OJ_Break_API.py/getSecondaryTypes?inst_id=6&format=json&key=FBF57A9F7A666FC0E0430100007F0CDC

==== getInstTaxa ====
===== Description =====
Get taxa and related taxonomic information from a selected institution.
===== Parameters =====
* ''inst_id'': number
* ''format'': string
* ''key'': string

===== Return =====
* ''taxa'': array of taxon_extended with below extension
** ''hier'': taxon_hierarchy

===== Example =====
https://osuc.biosci.ohio-state.edu/cgi-bin/OJ_Break_API.py/getInstTaxa?inst_id=21&format=json&key=FBF57A9F7A666FC0E0430100007F0CDC

==== getInstCollTrips2 ====
===== Description =====
Get collecting trip events and the specimen collected for a selected institution.
===== Parameters =====
* ''inst_id'': number
* ''format'': string
* ''key'': string

===== Return =====
* ''coll_trips'': array of taxon_basic, collection, collector, and loc_basic.

===== Example =====
https://osuc.biosci.ohio-state.edu/cgi-bin/OJ_Break_API.py/getInstCollTrips2?inst_id=21&format=json&key=FBF57A9F7A666FC0E0430100007F0CDC

==== getInstPubs ====
===== Description =====
Get published literature from a selected institution.
===== Parameters =====
* ''inst_id'': number
* ''format'': string
* ''key'': string

===== Return =====
* ''pubs'': array of literature_extended

===== Example =====
https://osuc.biosci.ohio-state.edu/cgi-bin/OJ_Break_API.py/getInstPubs?inst_id=1&format=json&key=FBF57A9F7A666FC0E0430100007F0CDC

=== Text Search ===
==== getSearchResults ====
===== Description =====
Get database results from a text keyword search.
===== Parameters =====
* ''name'': string
* ''limit'': number
* ''categoryLimit'': string
* ''format'': string
* ''key'': string

===== Return =====
* ''taxon_results'': array of below extensions
** ''taxa'': array of taxon_extended with below extension
*** ''lsid'': number
** ''count'': number
* ''cuid_results'': array of below extensions
** ''cuids'': array of cuids
** ''count'': number
* ''agent_results'': array of below extensions
** ''agents'': array of below extensions
*** ''type'': string
*** ''id'': number
*** ''name'': string
*** ''inst'': string
** ''count'': number
* ''inst_results'': array of below extensions
** ''inst'': array of collection_extended
** ''count'': number
* ''place_results'': array of below extensions
** ''places'': array of place with below extension
*** ''hier'': array of place
** ''count'': number
* ''journal_results'': array of below extensions
** ''journals'': array of below extensions
*** ''name'': string
*** ''id'': number
** ''count'': number

===== Example =====
https://osuc.biosci.ohio-state.edu/cgi-bin/OJ_Break_API.py/getSearchResults?name=%OSU%&limit=20&categoryLimit=&format=json&key=FBF57A9F7A666FC0E0430100007F0CDC

==== getTaxaFromText ====
===== Description =====
Get taxa results from a selected search keyword.
===== Parameters =====
* ''name'': string
* ''limit'': number
* ''nameOnly'': string
* ''format'': string
* ''key'': string

===== Return =====
* ''taxa'': array of taxon_extended with below extensions
** ''lsid'': number
* ''count'': number

===== Example =====
https://osuc.biosci.ohio-state.edu/cgi-bin/OJ_Break_API.py/getTaxaFromText?name=Heptascelio+striatosternus&limit=10&nameOnly=N&format=json&key=FBF57A9F7A666FC0E0430100007F0CDC

==== getCuidsFromText ====
===== Description =====
Get occurrence results from a selected search keyword.
===== Parameters =====
* ''name'': string
* ''limit'': number
* ''format'': string
* ''key'': string

===== Return =====
* ''cuids'': array of cuid
* ''count'': number

===== Example =====
https://osuc.biosci.ohio-state.edu/cgi-bin/OJ_Break_API.py/getCuidsFromText?name=%OSUC%&limit=10&format=json&key=FBF57A9F7A666FC0E0430100007F0CDC

==== getAgentsFromText ====
===== Description =====
Get agent (person and/or party) results from a selected search keyword.
===== Parameters =====
* ''name'': string
* ''limit'': number
* ''includeParty'': string
* ''format'': string
* ''key'': string

===== Return =====
* ''agents'': array of below elements
** ''id'': number
** ''type'': string
** ''name'': string
** ''inst'': string
* ''count'': number

===== Example =====
https://osuc.biosci.ohio-state.edu/cgi-bin/OJ_Break_API.py/getAgentsFromText?name=%Johnson,%20N.%20F.%&limit=10&includeParty=Y&format=json&key=FBF57A9F7A666FC0E0430100007F0CDC

==== getInstFromText ====
===== Description =====
Get institution/collection results from a selected search keyword(s).
===== Parameters =====
* ''name'': string
* ''limit'': number
* ''format'': string
* ''key'': string

===== Return =====
* ''inst'': array of collection_extended
* ''count'': number

===== Example =====
https://osuc.biosci.ohio-state.edu/cgi-bin/OJ_Break_API.py/getInstFromText?name=Hymenoptera&limit=10&format=json&key=FBF57A9F7A666FC0E0430100007F0CDC

==== getJournalsFromText ====
===== Description =====
Get journal results from a selected search keyword(s).
===== Parameters =====
* ''name'': string
* ''limit'': number
* ''format'': string
* ''key'': string

===== Return =====
* ''journals'': array of below elements
** ''name'': string
** ''id'': number
* ''count'': number

===== Example =====
https://osuc.biosci.ohio-state.edu/cgi-bin/OJ_Break_API.py/getJournalsFromText?name=Insect&limit=10&format=json&key=FBF57A9F7A666FC0E0430100007F0CDC

==== getOrgsFromText ====
===== Description =====
Get organization results for a selected search keyword(s).
===== Parameters =====
* ''name'': string
* ''limit'': number
* ''format'': string
* ''key'': string

===== Return =====
* ''orgs'': array of below elements
** ''name'': string
** ''id'': number
* ''count'': number

===== Example =====
https://osuc.biosci.ohio-state.edu/cgi-bin/OJ_Break_API.py/getOrgsFromText?name=%Geo%&limit=10&format=json&key=FBF57A9F7A666FC0E0430100007F0CDC

==== getPlacesFromText ====
===== Description =====

===== Parameters =====
* ''name'': string
* ''limit'': number
* ''format'': string
* ''key'': string

===== Return =====
* ''places'': array of place with below extension
** ''hier'': array of place
* ''count'': number

===== Example =====
https://osuc.biosci.ohio-state.edu/cgi-bin/OJ_Break_API.py/getPlacesFromText?name=Guyana&limit=10&format=json&key=FBF57A9F7A666FC0E0430100007F0CDC

==== getLocalitiesFromText ====
===== Description =====

===== Parameters =====
* ''name'': string
* ''limit'': number
* ''format'': string
* ''key'': string

===== Return =====
* ''locs'': array of below elements
** ''name'': string
** ''id'': number
* ''count'': number

===== Example =====
https://osuc.biosci.ohio-state.edu/cgi-bin/OJ_Break_API.py/getLocalitiesFromText?name=Guyana&limit=10&format=json&key=FBF57A9F7A666FC0E0430100007F0CDC

==== getCollMethodsFromText ====
===== Description =====

===== Parameters =====
* ''name'': string
* ''limit'': number
* ''format'': string
* ''key'': string

===== Return =====
* ''coll_methods'': array of below elements
** ''name'': string
** ''id'': number
* ''count'': number

===== Example =====
https://osuc.biosci.ohio-state.edu/cgi-bin/OJ_Break_API.py/getCollMethodsFromText?name=reared&limit=10&format=json&key=FBF57A9F7A666FC0E0430100007F0CDC

== Data Type Glossary ==
[[OJ_Break API Data Type Glossary]]

[[Category:OJ_Break API]]
[[Category:APIs]]

Museum Status

2018-06-19T16:45:01Z

Nfj:

<h2>Current System Status</h2>
DEA – Working to bring DEA back online.

HOL (And variants) – Mainly functional, however experiencing issues with exporting data. Investigating the issue.

HNS – Functional. Please report any further issues.

vSysLab – Function, Please report any further issues.

OSUC DB Mgr – Functional. Please report any further issues.

BLB – Functional. Please report any further issues.

Specimage – Functional. Please report any further issues.

If you encounter any issues, please email me at: britt.88@osu.edu

Museum Status

2018-06-19T16:44:34Z

Nfj:

Museum Status

2018-06-11T16:58:26Z

Nfj:

Museum Status

2018-06-11T15:44:48Z

Nfj:

Main Page

2018-06-11T15:40:39Z

Nfj:

Museum Status

2018-05-16T13:27:23Z

Nfj:

To help provide the most relevant information I have split this into two parts, the first being a brief status report on the current status of each application, followed by background information on the current roadblocks we are facing and the path to resolution.

Sites that are only experiencing errors related to mixed content / HTTPS can be accessed by bypassing the browser built-in security setting while using google chrome. A video demonstration can be seen here: https://www.youtube.com/watch?v=0abAq0BBUks

The two issue types commonly listed (CORS and HTTPS) we are waiting for OCIO to assist in resolving them.

<h1>Current System Status</h1>
DEA – Awaiting resolution of CORS to validate backend stability. Also requires HTTPS support before public usage. May potentially have backend issues, but will not be able to verify until the frontend of the system is functional.

HOL (And variants) – Experiencing HTTPS issues, see above video for how to bypass.

HNS – Experiencing HTTPS issues, see above video for how to bypass.

vSysLab – Experiencing HTTPS issues, see above video for how to bypass.

OSUC DB Mgr – Experiencing HTTPS issues and CORS issues.

BLB – Awaiting HTTPS and CORS for public access.

Specimage – Awaiting CORS for public access.

<h1>Background and current progress</h1>

I would first like to say that the database is online and fully functional, and all data contained within is restored and secure.

During the process of restoring the administrative applications we have encountered several critical security flaws that we had to halt our progress to resolve and work with David Sweasey of Risk Management and Governance to put exceptions in place to allow us to document and minimize the risk.

The security issues were already present within the database; however, it is only now that they have come to the surface. As we [ASCTechnology Services Application Development Team] are now maintaining and developing the database systems and related applications we are mandated to adhere to professional industry standard best practices to ensure the security and functionality of systems that we maintain. While we have been progressively working on improving a variety of areas behind the scenes over the last two months, the remaining issues that sites are experiencing is outlined below.

The first issue currently experienced by all applications is adding full support for HTTPS, which is the Hyper Text Transfer Protocol over Transport Layer Security. This standard dictates protocols and methodology for end-to-end encryption and identity verification of resources to protect against malicious attacks including:
- Sidejacking
- Packet Sniffing
- Session Hijacking
- Man-In-The-Middle
- Providing forward secrecy
- Content injection / manipulation
- Bad Router Attacks

We are mandated by our security offices to have all operations follow an HTTPS-Only standard configuration, and you can read more about why this is important and details of the benefits at the following information sites:
https://https.cio.gov/everything/
https://developers.google.com/web/fundamentals/security/encrypt-in-transit/why-https
https://en.wikipedia.org/wiki/HTTPS

Several applications are also currently experiencing issues with CORS, which is Cross Origin Resource Sharing. This is a series of standards and protocols that dictate the appropriate methodology to protect content providers and users from a variety of dangerous attacks, most notably XSS. XSS, otherwise known as Cross Site Scripting is a classification of attacks that allow malicious code injection into a user’s browser with goals ranging from session hijacking to privilege escalation. Cross Site Scripting has consistently placed highly on OWASP's Top 10 Web Security Threats list, since its inception in 2010. More information regarding the OWASP project can be found here: https://www.owasp.org/index.php/Category:OWASP_Top_Ten_Project
An outline of the most recent 2017 OWASP Top 10 Report can be seen at:
https://www.owasp.org/images/7/72/OWASP_Top_10-2017_%28en%29.pdf.pdf

A brief overview of other threats that can occur from CORS and their related risk are outlined here:
https://mobilejazz.com/blog/which-security-risks-do-cors-imply/

In addition, we are working to resolve issues related to Broken Authentification, allowing a malicious actor to impersonate an authorized user to gain access to an administrative system. This issue is primarily present within the OSUC DB Manager application.

The OSUC Manager application is currently one of our highest priorities and we are approaching the problem with a multi-pronged methodology utilizing resources from a variety college and university departments to bring it back online as quickly as possible. In addition to ASC Technology Services Application Development Team we are also receiving support from the OCIO Database Administrative Team to resolve the remaining HTTPS and CORS vulnerabilities and the ASC Director of IT Risk Managament and Governance David Sweasey to put IT Acknowledged Risk exceptions in place until the backend infrastructure can be rebuilt, creating a permanent resolution to the potential attack vectors.

We have also resolved a variety of additional security vulnerabilities over the last two months including Network Security, Firewall Security, System's Configuration Security, SELinux, VPN-Based Access Control, Data Retention Protocols, VEEAM Backups, and many other industry standard techniques and methods.

If you would like to further discuss any security related aspects of any MBD Applications that we are migrating to ASC Technology Services Infrastructure and the estimated timelines for full functionality to be restored for these projects, I would be happy to schedule a meeting with you to discuss this further.

Museum Status

2018-05-15T21:32:55Z

Nfj: Created page with "To help provide the most relevant information I have split this into two parts, the first being a brief status report on the current status of each application, followed by ba..."

To help provide the most relevant information I have split this into two parts, the first being a brief status report on the current status of each application, followed by background information on the current roadblocks we are facing and the path to resolution.

Sites that are only experiencing errors related to mixed content / HTTPS can be accessed by bypassing the browser built-in security setting while using google chrome. A video demonstration can be seen here: https://www.youtube.com/watch?v=0abAq0BBUks

The two issue types commonly listed (CORS and HTTPS) we are waiting for OCIO to assist in resolving them.

<h1>Current System Status</h1>
DEA – Awaiting resolution of CORS to validate backend stability. Also requires HTTPS support before public usage. May potentially have backend issues, but will not be able to verify until the frontend of the system is functional.
HOL (And variants) – Experiencing HTTPS issues, see above video for how to bypass.
HNS – Experiencing HTTPS issues, see above video for how to bypass.
vSysLab – Experiencing HTTPS issues, see above video for how to bypass.
OSUC DB Mgr – Experiencing HTTPS issues and CORS issues.
BLB – Awaiting HTTPS and CORS for public access.
Specimage – Awaiting CORS for public access.

<h1>Background and current progress</h1>

I would first like to say that the database is online and fully functional, and all data contained within is restored and secure.

During the process of restoring the administrative applications we have encountered several critical security flaws that we had to halt our progress to resolve and work with David Sweasey of Risk Management and Governance to put exceptions in place to allow us to document and minimize the risk.

The security issues were already present within the database; however, it is only now that they have come to the surface. As we [ASCTechnology Services Application Development Team] are now maintaining and developing the database systems and related applications we are mandated to adhere to professional industry standard best practices to ensure the security and functionality of systems that we maintain. While we have been progressively working on improving a variety of areas behind the scenes over the last two months, the remaining issues that sites are experiencing is outlined below.

The first issue currently experienced by all applications is adding full support for HTTPS, which is the Hyper Text Transfer Protocol over Transport Layer Security. This standard dictates protocols and methodology for end-to-end encryption and identity verification of resources to protect against malicious attacks including:
- Sidejacking
- Packet Sniffing
- Session Hijacking
- Man-In-The-Middle
- Providing forward secrecy
- Content injection / manipulation
- Bad Router Attacks

We are mandated by our security offices to have all operations follow an HTTPS-Only standard configuration, and you can read more about why this is important and details of the benefits at the following information sites:
https://https.cio.gov/everything/
https://developers.google.com/web/fundamentals/security/encrypt-in-transit/why-https
https://en.wikipedia.org/wiki/HTTPS

Several applications are also currently experiencing issues with CORS, which is Cross Origin Resource Sharing. This is a series of standards and protocols that dictate the appropriate methodology to protect content providers and users from a variety of dangerous attacks, most notably XSS. XSS, otherwise known as Cross Site Scripting is a classification of attacks that allow malicious code injection into a user’s browser with goals ranging from session hijacking to privilege escalation. Cross Site Scripting has consistently placed highly on OWASP's Top 10 Web Security Threats list, since its inception in 2010. More information regarding the OWASP project can be found here: https://www.owasp.org/index.php/Category:OWASP_Top_Ten_Project
An outline of the most recent 2017 OWASP Top 10 Report can be seen at:
https://www.owasp.org/images/7/72/OWASP_Top_10-2017_%28en%29.pdf.pdf

A brief overview of other threats that can occur from CORS and their related risk are outlined here:
https://mobilejazz.com/blog/which-security-risks-do-cors-imply/

In addition, we are working to resolve issues related to Broken Authentification, allowing a malicious actor to impersonate an authorized user to gain access to an administrative system. This issue is primarily present within the OSUC DB Manager application.

The OSUC Manager application is currently one of our highest priorities and we are approaching the problem with a multi-pronged methodology utilizing resources from a variety college and university departments to bring it back online as quickly as possible. In addition to ASC Technology Services Application Development Team we are also receiving support from the OCIO Database Administrative Team to resolve the remaining HTTPS and CORS vulnerabilities and the ASC Director of IT Risk Managament and Governance David Sweasey to put IT Acknowledged Risk exceptions in place until the backend infrastructure can be rebuilt, creating a permanent resolution to the potential attack vectors.

We have also resolved a variety of additional security vulnerabilities over the last two months including Network Security, Firewall Security, System's Configuration Security, SELinux, VPN-Based Access Control, Data Retention Protocols, VEEAM Backups, and many other industry standard techniques and methods.

If you would like to further discuss any security related aspects of any MBD Applications that we are migrating to ASC Technology Services Infrastructure and the estimated timelines for full functionality to be restored for these projects, I would be happy to schedule a meeting with you to discuss this further.

VSysLab :: Login, Logout

2016-11-04T14:12:05Z

Nfj: vSysLab login procedure

The URL to access vSysLab is [http://vsyslab.osu.edu vsyslab.osu.edu]. When you arrive there the page should look like this:<br><br>

[[File:vsyslablogin.jpg]]

Enter your username and password in the text boxes provided. If you are not a registered user and just want to see some of the features of vSysLab in action, then login using the username ASPGUEST and password ASPGUEST. This will provide you access to locked files in which you can see, but not change any data. If you would like to request an account to use vSysLab, press the button labeled "Sign up". That will take you to this form. Fill in the requested information, and you'll be manually added to the system.

[[File:AccountRequest.jpg]]

File:AccountRequest.jpg

2016-11-04T14:09:43Z

Nfj: Form for requesting an xBio:D account (and access to xBio:D web apps).

Form for requesting an xBio:D account (and access to xBio:D web apps).

VSysLab :: Login, Logout

2016-11-04T14:04:56Z

Nfj:

The URL to access vSysLab is [http://vsyslab.osu.edu vsyslab.osu.edu]. When you arrive there the page should look like this:

[[File:vsyslablogin.jpg]]

File:Vsyslablogin.jpg

2016-11-04T14:03:42Z

Nfj: vSysLab login page layout.

vSysLab login page layout.

VSysLab :: Login, Logout

2016-11-04T14:02:32Z

Nfj: Created page with "The URL to access vSysLab is [http://vsyslab.osu.edu vsyslab.osu.edu]. When you arrive there the page should look like this: File:Example.jpg"

The URL to access vSysLab is [http://vsyslab.osu.edu vsyslab.osu.edu]. When you arrive there the page should look like this:

[[File:Example.jpg]]

VSysLab Help

2016-11-04T13:49:53Z

Nfj: /* Frequently Asked Questions (FAQ) */

'''Introduction'''

This section contains information on how to use the virtual systematics lab web application named [http://vsyslab.osu.edu vSysLab], which is a part of the xBio:D cyberinfrastructure. This page includes instructions on how to manage OTUs and characters for a project, change determinations for specimens within the base taxon of a project, export a project in various data formats, and much more. To request a user account, create a new project, or suggest new features
to be added to vSysLab, contact [mailto:hol-help@osu.edu hol-help@osu.edu].

== Frequently Asked Questions (FAQ) ==
=== Getting Started ===
* Logging in and out - [[vSysLab :: Login, Logout]]
=== Publication Preparation ===
* How do I get the taxonomic history for a taxon? - [[vSysLab :: Generate Taxonomic History]]

== References ==

== Resources ==

[[Category:vSysLab]]

XBio:D Database Server Management

2016-10-28T18:00:04Z

Nfj:

----

'''xBio:D Database Server Management (osuc.biosci.ohio-state.edu)'''

== General Locations ==
* Apache Server Config: ''/etc/httpd/''
* Apache Web Directory: ''/var/www/''
* Oracle Home Directory: ''/opt/app/oracle/product/11.2.0/db_2''
* Oracle Base Directory: ''/opt/app/oracle''

== Applications / Services ==
* OJ_Break API - http://xbiod.osu.edu/OJ_Break/
* Database Gateway - http://osuc.biosci.ohio-state.edu/hymDB/
* LSID / GUID Metadata Handler - http://bioguid.osu.edu/
* xBio:D Javascript Library - http://xbiod.osu.edu/xbiod_lib/xbiod.js
* HOL - http://hol.osu.edu/
* vSysLab - http://vsyslab.osu.edu/
* DB Manager - http://osuc-mgr.osu.edu/
* HNS - http://hns.osu.edu/
* Platy site - osuc.biosci.ohio-state.edu/hymDB/eol_scelionidae.home
* HOL-based sites (Acarology, Bivalves, Fishes, UCFC)

== Startup Database ==

Although the database and all of the web services should automatically begin on startup, the database and its listener do not seem to obey. These instructions will provide you with information on starting the database. The assumption is that the user is already logged into the OSUC server.

# Startup the database:
## $ <code>sqlplus</code><br>
## $ <code>conn sys/password as sysdba /nolog</code><br>
## $ <code>dbstart $ORACLE_HOME</code>
# Start the database listener: $ <code>lsnrctl start</code>

Alternative:
# 01 Apr 2016 (no, this is <u>not</u> an April Fools joke)
## $ <code>sqlplus /nolog</code> // This connects to an idle instance
## $ <code>conn sys/password as sysdba</code><br>
## $ <code>startup</code>
# Start the database listener: $ <code>lsnrctl start</code>

I'm not sure how or why this worked, as we could not execute the first set of steps. For now, everything seems to be working. We'll see if that lasts.

== Database Backup ==
The database is backup up daily at 10PM via the db_backup.sh script. This script create a database dump using the ''exp'' command and transfers this file via FTP to the ''dumpfiles'' directory of the hymfiles web directory.

== Dataset Export ==
Data sets that are intended to be automatically updated in the xBio:D IPT must be specified within the ''export_dwca_collections.py'' found within the ''cgi-bin'' of the web server. Exports are placed into the data exports directory of the web server and present for harvesting by a supplementary script found on the hymfiles server where the IPT resides.

== Automatic File Cleanup ==

The database server hosts the xBio:D database, the APIs, HOL, vSysLab, DB Manager, HNS, and the various HOL-based sites, however the available hard disk space is somewhat limited. Trace and log files quickly fill up available space that requires a solution that addresses the issue periodically. There are two scripts on server that remove temporary files that may cause problems.
* The first script, removeOldTraceFiles.py, removes the Oracle trace files used by the optimizer to make database usage efficient. If trace files are older than five days, the script will remove these files to save space.
* The second script, removeOldDataExports.py, removes data exports from the various web applications. This script removes any export that has resided on the server for over a month.
[[Category:OSUC Private]]

XBio:D Database Server Management

2016-04-01T12:57:41Z

Nfj:

----

'''xBio:D Database Server Management (osuc.biosci.ohio-state.edu)'''

== General Locations ==
* Apache Server Config: ''/etc/httpd/''
* Apache Web Directory: ''/var/www/''
* Oracle Home Directory: ''/opt/app/oracle/product/11.2.0/db_2''
* Oracle Base Directory: ''/opt/app/oracle''

== Applications / Services ==
* OJ_Break API - http://xbiod.osu.edu/OJ_Break/
* Database Gateway - http://osuc.biosci.ohio-state.edu/hymDB/
* LSID / GUID Metadata Handler - http://bioguid.osu.edu/
* xBio:D Javascript Library - http://xbiod.osu.edu/xbiod_lib/xbiod.js
* HOL - http://hol.osu.edu/
* vSysLab - http://vsyslab.osu.edu/
* DB Manager - http://osuc-mgr.osu.edu/
* HNS - http://hns.osu.edu/
* Platy site - osuc.biosci.ohio-state.edu/hymDB/eol_scelionidae.home
* HOL-based sites (Acarology, Bivalves, Fishes, UCFC)

== Startup Database ==

Although the database and all of the web services should automatically begin on startup, the database and its listener do not seem to obey. These instructions will provide you with information on starting the database. The assumption is that the user is already logged into the OSUC server.

# Startup the database:
## $ <code>sqlplus</code><br>
## $ <code>conn sys/password as sysdba /nolog</code><br>
## $ <code>dbstart $ORACLE_HOME</code>
# Start the database listener: $ <code>lsnrctl start</code>

Alternative:
# 01 Apr 2016 (no, this is <u>not</u> an April Fools joke)
## $ <code>sqlplus /nolog</code> // This connects to an idle instance
## $ <code>conn sys/password as sysdba</code><br>
## $ <code>startup</code>

I'm not sure how or why this worked, as we could not execute the first set of steps. For now, everything seems to be working. We'll see if that lasts.

== Database Backup ==
The database is backup up daily at 10PM via the db_backup.sh script. This script create a database dump using the ''exp'' command and transfers this file via FTP to the ''dumpfiles'' directory of the hymfiles web directory.

== Dataset Export ==
Data sets that are intended to be automatically updated in the xBio:D IPT must be specified within the ''export_dwca_collections.py'' found within the ''cgi-bin'' of the web server. Exports are placed into the data exports directory of the web server and present for harvesting by a supplementary script found on the hymfiles server where the IPT resides.

== Automatic File Cleanup ==

The database server hosts the xBio:D database, the APIs, HOL, vSysLab, DB Manager, HNS, and the various HOL-based sites, however the available hard disk space is somewhat limited. Trace and log files quickly fill up available space that requires a solution that addresses the issue periodically. There are two scripts on server that remove temporary files that may cause problems.
* The first script, removeOldTraceFiles.py, removes the Oracle trace files used by the optimizer to make database usage efficient. If trace files are older than five days, the script will remove these files to save space.
* The second script, removeOldDataExports.py, removes data exports from the various web applications. This script removes any export that has resided on the server for over a month.
[[Category:OSUC Private]]

XBio:D Database Server Management

2016-04-01T12:56:54Z

Nfj:

----

'''xBio:D Database Server Management (osuc.biosci.ohio-state.edu)'''

== General Locations ==
* Apache Server Config: ''/etc/httpd/''
* Apache Web Directory: ''/var/www/''
* Oracle Home Directory: ''/opt/app/oracle/product/11.2.0/db_2''
* Oracle Base Directory: ''/opt/app/oracle''

== Applications / Services ==
* OJ_Break API - http://xbiod.osu.edu/OJ_Break/
* Database Gateway - http://osuc.biosci.ohio-state.edu/hymDB/
* LSID / GUID Metadata Handler - http://bioguid.osu.edu/
* xBio:D Javascript Library - http://xbiod.osu.edu/xbiod_lib/xbiod.js
* HOL - http://hol.osu.edu/
* vSysLab - http://vsyslab.osu.edu/
* DB Manager - http://osuc-mgr.osu.edu/
* HNS - http://hns.osu.edu/
* Platy site - osuc.biosci.ohio-state.edu/hymDB/eol_scelionidae.home
* HOL-based sites (Acarology, Bivalves, Fishes, UCFC)

== Startup Database ==

Although the database and all of the web services should automatically begin on startup, the database and its listener do not seem to obey. These instructions will provide you with information on starting the database. The assumption is that the user is already logged into the OSUC server.

# Startup the database:
## $ <code>sqlplus</code><br>
## $ <code>conn sys/password as sysdba /nolog</code><br>
## $ <code>dbstart $ORACLE_HOME</code>
# Start the database listener: $ <code>lsnrctl start</code>

# 01 Apr 2016 (no, this is <u>not</u> and April Fools joke)
## $ <code>sqlplus /nolog</code> // This connects to an idle instance
## $ <code>conn sys/password as sysdba</code><br>
## $ <code>startup</code>

I'm not sure how or why this worked, as we could not execute the first set of steps. For now, everything seems to be working. We'll see if that lasts.

== Database Backup ==
The database is backup up daily at 10PM via the db_backup.sh script. This script create a database dump using the ''exp'' command and transfers this file via FTP to the ''dumpfiles'' directory of the hymfiles web directory.

== Dataset Export ==
Data sets that are intended to be automatically updated in the xBio:D IPT must be specified within the ''export_dwca_collections.py'' found within the ''cgi-bin'' of the web server. Exports are placed into the data exports directory of the web server and present for harvesting by a supplementary script found on the hymfiles server where the IPT resides.

== Automatic File Cleanup ==

The database server hosts the xBio:D database, the APIs, HOL, vSysLab, DB Manager, HNS, and the various HOL-based sites, however the available hard disk space is somewhat limited. Trace and log files quickly fill up available space that requires a solution that addresses the issue periodically. There are two scripts on server that remove temporary files that may cause problems.
* The first script, removeOldTraceFiles.py, removes the Oracle trace files used by the optimizer to make database usage efficient. If trace files are older than five days, the script will remove these files to save space.
* The second script, removeOldDataExports.py, removes data exports from the various web applications. This script removes any export that has resided on the server for over a month.
[[Category:OSUC Private]]

Main Page

2015-12-10T16:25:03Z

Nfj: /* Insect Collection (OSUC) Private Portal */

Main Page

2015-12-10T16:22:48Z

Nfj:

'''Welcome to the xBio:D Help Wiki at the Ohio State University'''

This wiki is a semi-protected wiki with only verified users able to manipulate the contents. If you are a user and would like to become verified, contact [mailto:hol-help@osu.edu hol-help@osu.edu] and request a change in status. Please contribute any additional knowledge to the wiki pages to ensure a more greatly informed base of users.

== Insect Collection (OSUC) Protocols (internal use only) ==
* [[Sorting Platygastroidea Identified Material]]
* [[Hymenoptera Cataloging Workflow]]
* [[Annotating Publications]]
* [[Extended-Focus Imaging Using Auto-Montage System]]

== Insect Collection (OSUC) Private Portal ==
* [[Collection (OSUC) Private Portal]]

== xBio:D Web Services Help ==
=== Applications ===
* [[Data Entry Assistant (DEA) Help]]
* [[vSysLab Help]]
* [[Database Manager Help]]
* [[Specimage Help]]
* [[Hymenoptera Online (HOL) Help]]

=== APIs ===
* [[xBio:D Javascript Library Reference]]
* [[OJ_Break API Reference]]
* [[OJ_Break Version 2 API Reference]]

=== Collaborators ===
* [[xBio:D Occurrence Collaborators]]
* [[xBio:D Taxonomic Collaborators]]
* [[xBio:D Literature Collaborators]]
* [[xBio:D Media Collaborators]]

== Fish Collection (OSUM) Protocols ==
* [[Data Entry Procedures]]

== Ohio Biodiversity Conservation Partnership (OBCP) Informatics Portal ==
* [[OBCP Informatics Portal]]

== Trissolcus / Stinkbug Information Portal ==
* [[Trissolcus / Stinkbug Procedures]]

Extended-Focus Imaging Using Auto-Montage System

2015-12-10T16:21:57Z

Nfj: Protected "Extended-Focus Imaging Using Auto-Montage System" ([Edit=OSUC users group] (indefinite) [Move=OSUC users group] (indefinite) [Read=OSUC users group] (indefinite))

'''Introduction'''

This section contains procedures for taking and creating extended-focusing images using an Auto-Montage imaging system. The procedures were initially described by Elijah Talamas.

== Specimen Configuration / Initial Setup ==
=== Mount Specimen in Clay ===
Adjust the specimen in clay into the appropriate position for imaging. It is usually necessary to do this under a microscope.

=== Place Specimen onto Stage ===
Center the specimen directly beneath the camera lens and orient it by eye as best you can.

=== Orient Light Dome ===
Place light dome over the specimen. Be sure that the camera is sufficiently raised to avoid a collision between the light dome and the camera/lens. Also, be sure not to hit the specimen with the light dome or scratch the interior of the light dome with the end of the insect pin. Now, turn on the light dome

=== Fine-tune Specimen Orientation ===
Lower the camera/lens to bring the insect into focus. You may have to increase or decrease the exposure time to see the insect, particularly when it is out of focus. Make the final fine-tune adjustments to the orientation of the specimen. Fine movements along the stage are best achieved by the adjustment knobs in the back right corner of the imaging stage. To perform rotational movement, firmly and slowly rotate the stage by holding onto it on opposite ends.

=== Adjust Light Settings ===
Adjust the light settings (see [[#Lighting|Lighting]]).

== Imaging ==
Use either one of the two imaging approaches as defined below.

=== Taking Individual Images (Stack) Manually ===
Using either the coarse or fine adjustment setting (depending on magnification), find the highest point of the specimen that you want to be in focus in your final product. Now begin to image by taking photographs incrementally (press ''Capture'' to take the photograph under the fine adjustment setting. Watch closely at a point that is in focus as you move the camera; just as it becomes out of focus and a point below or above it begins to come into focus is when you should take the photo. It is helpful to follow the area of focus along a continuous surface, like an antenna, wing, or leg, as you move through the depth of the specimen. Your last photograph will be at the lowest point of the specimen that you desire to be in focus in your final product. This process requires experience to master.

[[File:capture.png|none|frame|Take photographs by pressing Capture]]

=== Taking Individual Images (Stack) with Z-Stepper ===
Note: Z-stepper on the OSUC Auto-Montage machine is inoperable!

== Extended-Focus Image Processing ==
=== Using Auto-Montage Software ===
==== Create Extended-Focus Image ====
Load the source images, they will automatically be loaded if you just took them. Press the blue ''M'' icon to begin the montage process. You will now see an option to select the type of algorithm and the spot size. The algorithm is typically set to ''Blended''. A small spot size will often produce a better image, yet will require extensive cleanup. A large spot size typically reduces the need for cleanup but also reduces detail in the final image. If you are a beginner, use 15 for the spot size, and change it as you see fit for different specimens, experimentation, etc. Now, press the ''Scan'' button and wait for the program to combine the images.

[[File:montage-button.png|left|frame|Begin montage process]]
[[File:scan-dialog.png|none|frame|Specify settings then press Scan]]

==== Image Clean Up ====
Select ''Tile Vertically'' from the ''Window'' menu.
[[File:tile-vertically.png|none|frame|Arrange source images (stack)]]

From here you may select from one of the source images to clean up the montage image if necessary (refer to the image below for number references). This may be done in two ways:
# Using the paint brush tool (#1), this is best for small areas. 3 sizes are available (#7).
# Using the area selection tool, this is best for large areas (#2 and #3). You may select either the interior (#4) or exterior (#5) of the area to be replaced by the source image.
[[File:AM-toolbar.png|none|frame|Annotated Auto-Montage toolbar]]

To select the source image that will be used to replace the corresponding area on the montage image, first scroll through the source images until you find which one is the best. You can do this easily be clicking on the lower right corner (#1 below) and using the mouse wheel to scroll up and down through the images. If you now click the paint brush or area selection tool, then the source image you see is the one selected. If not, or if you have clicked elsewhere, you may select the image using the eyedropper tool (#6 above). It does not matter if you use the tools on the source image or the montage image during cleanup- the result is the same. It may help to increase or decrease the zoom. This can be adjusted by the sliding bar in the upper right hand corner (#2 below).
[[File:AM-tile-view.png|none|frame|Vertical tiles during clean up]]

==== Applying Scalebar / Measuring ====
Now that you have cleaned up the image, select the appropriate magnification to calibrate the image (#3 above). A scalebar will appear on the image. It is best to move this to a place where it does not overlap the specimen so that it may be easily removed in Photoshop for publication. Placing the mouse cursor over the scalebar will transform it into a hand tool for moving.

Now that the montage image is properly calibrated, you can measure anything you wish using the straight line ruler (#1 below), zig-zag line ruler (#2 below), or lasso ruler (#3 below). Press the ''Measurement Details'' button (#4 below) to see the results, and delete measurement lines with the delete button (#5 below).
[[File:measurements.png|none|frame|View during measurements]]

==== Save Image ====
Save the montage image and montage file (''.m'' extension) if you will need to do measurements in the future. Save the source images if you think you will need to do clean up in the future, or if you need them for another purpose. Typically, these are deleted once you produce a satisfactory montage image. Export the montage image, with scalebar, as a TIF file.

==== Specimage Upload ====
Upload the image into [http://specimage.osu.edu Specimage] immediately. Record the label data immediately and send this information to [mailto:cora.1@osu.edu Joe Cora].

=== Using Combine ZP Software ===
==== Create Extended-Focus Image ====
Start the program. Click ''New''. Select all of the appropriate source images and click ''Open''. Select ''Do Stack'' from the main menu and press ''Go''. Wait for the extended-focus processing to complete.

==== Save Image without Scalebar ====
Click the button showing a rectangular dotted line. You will then see a dotted line surround the image. Save as either a JPG or a TIF file. To add a scale bar you will need to open the image file in Automontage- it is a good idea to record the magnification setting of the lens in the filename so that you do not make mistakes, i.e. filename= ''lateralhead_1-25.jpg'', where the magnification setting of the camera is at 1.25.

==== Applying Scalebar in Auto-Montage ====
If you saved the image as a JPG, then open it in Automontage by selecting ''single montage image''. If you saved as a TIF then you will have to open it in Photoshop and resave it without alpha channels in order for it to open properly in Automontage. Once you have opened the file in Automontage, calibrate the image appropriately. Once the image is properly calibrated, apply the scalebar as described above (see [[#Applying Scalebar / Measuring|Applying Scalebar / Measuring]]) and follow the additional steps (see [[#Save Image|Save Image]] and [[#Specimage Upload|Specimage Upload]]).
[[File:single-image-save.png|none|frame|Selecting single montage image]]

== Lighting ==
=== Adjust Brightness ===
You can adjust the brightness while taking images in 3 ways.
* Increase or decrease the exposure time of the camera.
[[File:exposure.png|none|frame|Adjust exposure time]]
* Increase or decrease the light intensity in the light dome.
[[File:light-dome-adjustments.png|none|frame|Adjust light intensity]]
* Increase or decrease the size of the lens aperture.
[[File:aperture-adjustment.png|none|frame|Adjust lens aperture]]

=== Adjust Color Scheme ===
You can adjust the color scheme while taking images in three ways by selecting Settings from the ''Capture'' window
[[File:capture-settings.png|none|frame|Settings button for image capture]]

* White balance: this can be set manually, automatically, or you can use Preset settings: 3200K for yellower light, such as halogen light sources, or 5600K for bluer light, such as the light dome. The ''PRESET'' setting must be selected for these to work properly. Preset settings are recommended.
[[File:white-balance.png|none|frame|White balance settings]]

* Image Settings:
# Alter the gamma levels. This will change the relative brightness of shadows.
# Alter the Master Black: If this level is set too low, the entire image will appear darker than it should (the image will appear blackish and heavier). If the level is set too high on the other hand, the image will look lighter than it should (the image will look foggy with less contrast).

[[Category:Specimage]]

Annotating Publications

2015-12-10T16:21:29Z

Nfj: Protected "Annotating Publications" ([Edit=OSUC users group] (indefinite) [Move=OSUC users group] (indefinite) [Read=OSUC users group] (indefinite))

'''Introduction'''

This section contains procedures and conventions used for annotating taxonomic acts within publications.

== General Notes ==
* All annotation text must be in lowercase except for proper nouns, taxonomic names, and after certain special cases where periods are used (i.e. original descriptions of genera). The first letter of an annotation is not capitalized.
* Always use the spelling as it is used in a publication with abbreviations spelled out fully (e.g. ''Tel. (A.) adenyus'' -> ''Telenomus (Aholcus) adenyus''). When a taxon name is misspelled, include only the taxonomic acts that use the misspelled name and include ''spelling error'' in the annotation text.
* The pages for an annotation are always listed from first (lowest) page to last (highest) page.
* Rank the individual acts within the annotation text according to level of importance
** ''original description'' > ''generic transfer'' > ''replacement name'' > ''description'' > ''diagnosis'' > ''synonymy'' or ''jr. synonym'' > ''key to {group}'' > ''keyed'' > ''type information'' or ''lectotype designation'' > ...
* The page number used for an annotation is the first page on which a taxonomic act appears.
** An original description begins with the header containing the newly described name of a descriptive block.
* For keys, every page on which a taxon is keyed is listed in the pages for an annotation.
* If a key, catalog, revision, etc. is limited in scope by geographic region, sex of specimens, or any other faction, include the qualified terms in the annotation text.
** Common qualified annotations are: ''key to the Nearctic species for males'', ''catalog of New World genera'', etc.

== Annotation Text Reference ==
{|
!Taxonomic Act
!Annotation Text
!Comments
|-
|original description of a species-group taxon
|''original description''
|Note: When using the ''original description'' annotation, the assumption is that the name is code-compliant and available.
|-
|original description of a genus-group taxon
|''original description. Type: {type species w/ author}, by monotypy and/or original designation or designated by {author} ({year})''
|Examples: ''original description. Type: Embioctonus setiger Masner, by monotypy and original designation''; ''original description. Type: Anteris bilineata Thomson, designated by Muesebeck & Walkley (1956)''. Note: When using the ''original description'' annotation, the assumption is that the name is code-compliant and available.
|-
|original description of a family-group taxon
|''original description''
|Note: When using the ''original description'' annotation, the assumption is that the name is code-compliant and available.
|-
|removed from synonymy with another taxon
|''removed from synonymy with {taxon w/ author}''
|
|-
|subgeneric or subspecific designation
|''changed to {subgeneric or subspecific} status''
|
|-
|species-group taxon is transferred to another genus
|''generic transfer''
|
|-
|replacement name (nomen nova) for homonym
|''replacement name for {taxon w/ author}''
|
|-
|junior subjective synonym replaces newly recognized homonym as valid name
|''senior available for {taxon w/ author}''
|
|-
|name is recognized as a junior homonym
|''recognized as junior homonym of {taxon w/ author}''
|
|-
|taxon is redescribed
|''description''
|
|-
|taxon is diagnosed
|''diagnosis''
|
|-
|taxon is senior synonym of taxon (new synonyms only)
|''synonymy''
|
|-
|taxon is junior synonym of taxon (new synonyms only)
|''junior synonym of {valid taxon w/ author}''
|
|-
|key is provided for subordinate taxa
|''key to {group}''
|Examples: ''key to species'', ''key to tribes of Madagascar'', etc.
|-
|taxon is keyed
|''keyed''
|
|-
|subsequent primary type designation
|''{lectotype or neotype} designation''
|If used, do not include ''type information'' annotation
|-
|primary type of a species-group taxon is identified
|''type information''
|
|-
|primary type of a species-group taxon is lost
|''type lost''
|If used, do not include ''type information'' annotation
|-
|primary type of a species-group taxon is destroyed
|''type destroyed''
|If used, do not include ''type information'' annotation
|-
|taxon placed within higher order taxon or informal group
|''placed in {taxon or informal group}''
|Note: Do not included this annotation text if a subgenus is explicitly used within the taxon name (''Telenomus (Aholcus) anantes''). Examples: ''placed in Telenomus (Aholcus)'', ''placed in Trissolcus basalis species gp.'', ''placed in Baryconini'', etc.
|-
|new distribution record
|''new distribution record for {place}''
|
|-
|catalog of subordinate taxa for the means of presenting a list of taxa
|''catalog of {qualifier}''
|Catalogs are usually made of a specific scope like ''catalog of New Word species'' or ''catalog of species described by G. Mayr''.
|-
|taxon listed in a catalog
|''listed''
|
|-
|biological association of a taxon that has not previously been identified
|''host association''
|Separately in the annotation spreadsheet, mark the page number and the associated taxa which are being identified for host annotating.
|-
|new name did not meet the criteria for availability as defined in the [http://www.nhm.ac.uk/hosted-sites/iczn/code/ ICZN].
|''described as new, unavailable: {reason}''
|Examples: ''described as new, unavailable: type species not specified'', ''described as new, unavailable name: type depository not specified'', etc.
|}

== Taxonomic Act Glossary ==
;description
: The act of describing the morphological or other salient characters of a taxon.
;diagnosis
: The act of defining characters that distinguishes a taxon from another taxon.
;junior synonym
: A taxon that is treated to be the same as another taxon in which the later taxon is older and considered to be the valid name.
;primary type
: The name-bearing type for a species-group taxon, which includes holotype, lectotype, neotype, and syntype.

== Resources ==
* Annotation Template (Windows-only): [[File:Annotations.xls‎]]

[[Category:Database Manager]]
[[Category:Hymenoptera Catalog]]

Hymenoptera Cataloging Workflow

2015-12-10T16:21:00Z

Nfj: Protected "Hymenoptera Cataloging Workflow" ([Edit=OSUC users group] (indefinite) [Move=OSUC users group] (indefinite) [Read=OSUC users group] (indefinite))

'''Introduction'''

This section contains the workflow used to catalog the names, taxonomic acts, and literature of the Hymenoptera. The workflow is broken into steps that should be followed sequentially.

== Catalog Acquisition / Processing ==
=== Overview ===
Many groups already have printed catalogs that should be used as a backbone for a group. We begin by finding a printed copy of the catalog and scan it at 600 dpi. The high level of resolution required for the scanning ensures a quality OCR of the text.

=== Steps ===
* Scan catalog at 600 dpi
* [[OCR PDF with ABBYY]]

== Taxonomic Name Entry ==
TODO

== Literature Reference Entry / PDF Upload ==
TODO

== Literature Annotation ==
TODO

[[Category:Hymenoptera Catalog]]

Sorting Platygastroidea Identified Material

2015-12-10T16:20:24Z

Nfj: Protected "Sorting Platygastroidea Identified Material" ([Edit=OSUC users group] (indefinite) [Move=OSUC users group] (indefinite) [Read=OSUC users group] (indefinite))

'''Introduction'''

This section contains procedures for handling Platygastroidea material that has been identified and whose specimen data has been transcribed.

== Procedures ==

=== Sorting Individual Drawers ===
# Remove a drawer from cabinet one. Make sure it is a drawer that has been sort to genus, not just to family.
# Grab a drawer of unit trays for the material to be sorted into from cabinet seven.
#* Make sure you have a good mixture of small and medium-sized soft unit trays and one hard-bottomed tray to place excess labels in.
# Scan the drawer of specimens to be sorted and look for the first alphabetically. Working your way through the drawer, remove all specimens of that type and place them together in a single unit tray
#*If there are too many to fit in one unit try, move onto a second, but do not forget to place a label at the upper left corner of that tray as well.
#*If a row of specimens has a determination label at the beginning, do not mix those in even with specimens of the same genus. They can be placed in the same unit try but must remain separate.
# Continue this process until all specimens are sorted alphabetically by genus.
#* When you come across any of the genera listed on the [[Target Taxa#Target List|Target List]], any genus followed by MS or preceded by "nr.", or sorted into the subfamilies Scelioninae, Telenominae, or Teleasinae, make sure to remove them and place them in the VIBs (Very Important Bugs) Drawer located toward the bottom of cabinet one.
# After you have sorted two or three individual drawers into genus, you may choose to combine these drawers together (using similar protocol as above) as this will make the next step more efficient.
*If you come across insects that are oriented in different directions, do not orient them in the same direction. Retain the original orientation as this denotes gender. Also, in regards to gender, when you come across tags with the male or female symbols, keep these specimens grouped together. For example, if you have a male symbol followed by five specimens, do not just begin to place other, unsexed material after the fifth male. Instead, place another label after the fifth and then begin to add the other specimens.

=== Sorting into Alphabetized Drawers ===
# In cabinet eight, you will see a few dozen drawers with letters on the front. Scan your sorted genera and use the carts to grab the first four or five drawers you will need.
#* It is actually time-saving to note which drawers will be necessary. For example, if you grabbed drawers A through F but you did not have any genera that began with 'B' to place in them, you have made unnecessary work for yourself.
#* Some drawers in cabinet eight will be used specifically for one genus. This if often the case for genera of which the collection has many, i.e., Telenomus. When these become full, follow the instructions in the [[#Sorting Full Drawers Containing a Single Genus|next subsection]].
# Place the genera into the correctly labeled drawers, trying to keep them in alphabetical order within the new drawers as well. When you have finished with the first load, take them back and continue the process until all genera have been sorted into cabinet eight.
#* If you come across a specimen that does not belong to OSUC, as indicated by a colored tag on the pin, you will need to sort them in a similar fashion into the Collections drawers located in cabinets nine and ten.

==== Sorting Full Drawers Containing a Single Genus ====
When you fill a drawer in cabinet eight with a single genus, remove that drawer and sort the genus into the locations in which it was collected. Certain locations will usually go into certain collections, most have tags denoting the collection they are part of, or in ROME's case have a ROM number or IIS number on the insect label, but for those that do not, here is a rough categorization of where they go:
*OSUC:
**North American: Virgin Islands, Mexico - P&K
**South America: Belize, Chile, Colombia (M#s),
**Africa: South Africa - collected by Philips, Tunisia
**Europe: Sweden, Italy, Spain
**Asia: Russia, Israel, Thailand (T#s)
***For Costa Rican, New Caledonian (and South African material collected by Irwin), Paraguayan, and some Brazilian specimens, they will have to be separated out and place in the proper cabinets in the fourth row.
*IZIKO
**Africa: South African - collected by van Noort
As always, you have any question in your mind about what to do, ask before you take any action.

''*Add notes for where to put specimens after sorted into collections/localities''

=== Labels ===
*When sorting different trays of the same genus together, you may remove excess labels and consolidate the specimens.
*Do not remove labels if:
#The label is a determination label.
#The insects come from different collections.
*Handwritten labels (except for determination labels), excess collection labels, and excess gender tags may be discarded and the pins sorted into their correct vials in the red boxes located in the blue shelves near Joe.
*Typed labels will be saved and sorted into the drawer marked 'Labels' in cabinet seven.

== Resources ==
* [[Target Taxa]]

Main Page

2015-12-10T16:16:15Z

Nfj:

'''Welcome to the xBio:D Help Wiki at the Ohio State University'''

This wiki is a semi-protected wiki with only verified users able to manipulate the contents. If you are a user and would like to become verified, contact [mailto:hol-help@osu.edu hol-help@osu.edu] and request a change in status. Please contribute any additional knowledge to the wiki pages to ensure a more greatly informed base of users.

== Insect Collection (OSUC) Private Portal ==
* [[Collection (OSUC) Private Portal]]

== xBio:D Web Services Help ==
=== Applications ===
* [[Data Entry Assistant (DEA) Help]]
* [[vSysLab Help]]
* [[Database Manager Help]]
* [[Specimage Help]]
* [[Hymenoptera Online (HOL) Help]]

=== APIs ===
* [[xBio:D Javascript Library Reference]]
* [[OJ_Break API Reference]]
* [[OJ_Break Version 2 API Reference]]

=== Collaborators ===
* [[xBio:D Occurrence Collaborators]]
* [[xBio:D Taxonomic Collaborators]]
* [[xBio:D Literature Collaborators]]
* [[xBio:D Media Collaborators]]

== Insect Collection (OSUC) Protocols ==
* [[Sorting Platygastroidea Identified Material]]
* [[Hymenoptera Cataloging Workflow]]
* [[Annotating Publications]]
* [[Extended-Focus Imaging Using Auto-Montage System]]

== Fish Collection (OSUM) Protocols ==
* [[Data Entry Procedures]]

== Ohio Biodiversity Conservation Partnership (OBCP) Informatics Portal ==
* [[OBCP Informatics Portal]]

== Trissolcus / Stinkbug Information Portal ==
* [[Trissolcus / Stinkbug Procedures]]

XBio:D Database Server Management

2015-10-21T20:37:00Z

Nfj: /* Startup Database */

----

'''xBio:D Database Server Management (osuc.biosci.ohio-state.edu)'''

== General Locations ==
* Apache Server Config: ''/etc/httpd/''
* Apache Web Directory: ''/var/www/''
* Oracle Home Directory: ''/opt/app/oracle/product/11.2.0/db_2''
* Oracle Base Directory: ''/opt/app/oracle''

== Applications / Services ==
* OJ_Break API - http://xbiod.osu.edu/OJ_Break/
* Database Gateway - http://osuc.biosci.ohio-state.edu/hymDB/
* LSID / GUID Metadata Handler - http://bioguid.osu.edu/
* xBio:D Javascript Library - http://xbiod.osu.edu/xbiod_lib/xbiod.js
* HOL - http://hol.osu.edu/
* vSysLab - http://vsyslab.osu.edu/
* DB Manager - http://osuc-mgr.osu.edu/
* HNS - http://hns.osu.edu/
* Platy site - osuc.biosci.ohio-state.edu/hymDB/eol_scelionidae.home
* HOL-based sites (Acarology, Bivalves, Fishes, UCFC)

== Startup Database ==

Although the database and all of the web services should automatically begin on startup, the database and its listener do not seem to obey. These instructions will provide you with information on starting the database. The assumption is that the user is already logged into the OSUC server.

# Startup the database:
## $ <code>sqlplus</code><br>
## $ <code>conn sys/password as sysdba /nolog</code><br>
## $ <code>dbstart $ORACLE_HOME</code>
# Start the database listener: $ <code>lsnrctl start</code>

== Database Backup ==
The database is backup up daily at 10PM via the db_backup.sh script. This script create a database dump using the ''exp'' command and transfers this file via FTP to the ''dumpfiles'' directory of the hymfiles web directory.

== Dataset Export ==
Data sets that are intended to be automatically updated in the xBio:D IPT must be specified within the ''export_dwca_collections.py'' found within the ''cgi-bin'' of the web server. Exports are placed into the data exports directory of the web server and present for harvesting by a supplementary script found on the hymfiles server where the IPT resides.

== Automatic File Cleanup ==

The database server hosts the xBio:D database, the APIs, HOL, vSysLab, DB Manager, HNS, and the various HOL-based sites, however the available hard disk space is somewhat limited. Trace and log files quickly fill up available space that requires a solution that addresses the issue periodically. There are two scripts on server that remove temporary files that may cause problems.
* The first script, removeOldTraceFiles.py, removes the Oracle trace files used by the optimizer to make database usage efficient. If trace files are older than five days, the script will remove these files to save space.
* The second script, removeOldDataExports.py, removes data exports from the various web applications. This script removes any export that has resided on the server for over a month.
[[Category:OSUC Private]]

XBio:D Database Server Management

2015-10-21T20:36:01Z

Nfj: /* Startup Database */

----

'''xBio:D Database Server Management (osuc.biosci.ohio-state.edu)'''

== General Locations ==
* Apache Server Config: ''/etc/httpd/''
* Apache Web Directory: ''/var/www/''
* Oracle Home Directory: ''/opt/app/oracle/product/11.2.0/db_2''
* Oracle Base Directory: ''/opt/app/oracle''

== Applications / Services ==
* OJ_Break API - http://xbiod.osu.edu/OJ_Break/
* Database Gateway - http://osuc.biosci.ohio-state.edu/hymDB/
* LSID / GUID Metadata Handler - http://bioguid.osu.edu/
* xBio:D Javascript Library - http://xbiod.osu.edu/xbiod_lib/xbiod.js
* HOL - http://hol.osu.edu/
* vSysLab - http://vsyslab.osu.edu/
* DB Manager - http://osuc-mgr.osu.edu/
* HNS - http://hns.osu.edu/
* Platy site - osuc.biosci.ohio-state.edu/hymDB/eol_scelionidae.home
* HOL-based sites (Acarology, Bivalves, Fishes, UCFC)

== Startup Database ==

Although the database and all of the web services should automatically begin on startup, the database and its listener do not seem to obey. These instructions will provide you with information on starting the database. The assumption is that the user is already logged into the OSUC server.

# Startup the database:

$ <code>sqlplus</code><br>
$ <code>conn sys/password as sysdba /nolog</code><br>
$ <code>dbstart $ORACLE_HOME</code>

# Start the database listener: $ <code>lsnrctl start</code>

== Database Backup ==
The database is backup up daily at 10PM via the db_backup.sh script. This script create a database dump using the ''exp'' command and transfers this file via FTP to the ''dumpfiles'' directory of the hymfiles web directory.

== Dataset Export ==
Data sets that are intended to be automatically updated in the xBio:D IPT must be specified within the ''export_dwca_collections.py'' found within the ''cgi-bin'' of the web server. Exports are placed into the data exports directory of the web server and present for harvesting by a supplementary script found on the hymfiles server where the IPT resides.

== Automatic File Cleanup ==

The database server hosts the xBio:D database, the APIs, HOL, vSysLab, DB Manager, HNS, and the various HOL-based sites, however the available hard disk space is somewhat limited. Trace and log files quickly fill up available space that requires a solution that addresses the issue periodically. There are two scripts on server that remove temporary files that may cause problems.
* The first script, removeOldTraceFiles.py, removes the Oracle trace files used by the optimizer to make database usage efficient. If trace files are older than five days, the script will remove these files to save space.
* The second script, removeOldDataExports.py, removes data exports from the various web applications. This script removes any export that has resided on the server for over a month.
[[Category:OSUC Private]]

XBio:D Database Server Management

2015-10-21T20:35:05Z

Nfj:

----

'''xBio:D Database Server Management (osuc.biosci.ohio-state.edu)'''

== General Locations ==
* Apache Server Config: ''/etc/httpd/''
* Apache Web Directory: ''/var/www/''
* Oracle Home Directory: ''/opt/app/oracle/product/11.2.0/db_2''
* Oracle Base Directory: ''/opt/app/oracle''

== Applications / Services ==
* OJ_Break API - http://xbiod.osu.edu/OJ_Break/
* Database Gateway - http://osuc.biosci.ohio-state.edu/hymDB/
* LSID / GUID Metadata Handler - http://bioguid.osu.edu/
* xBio:D Javascript Library - http://xbiod.osu.edu/xbiod_lib/xbiod.js
* HOL - http://hol.osu.edu/
* vSysLab - http://vsyslab.osu.edu/
* DB Manager - http://osuc-mgr.osu.edu/
* HNS - http://hns.osu.edu/
* Platy site - osuc.biosci.ohio-state.edu/hymDB/eol_scelionidae.home
* HOL-based sites (Acarology, Bivalves, Fishes, UCFC)

== Startup Database ==

Although the database and all of the web services should automatically begin on startup, the database and its listener do not seem to obey. These instructions will provide you with information on starting the database. The assumption is that the user is already logged into the OSUC server.

# Startup the database:

$ <code>sqlplus</code>
$ <code>conn sys/password as sysdba /nolog</code>
$ <code>dbstart $ORACLE_HOME</code>

# Start the database listener: $ <code>lsnrctl start</code>

== Database Backup ==
The database is backup up daily at 10PM via the db_backup.sh script. This script create a database dump using the ''exp'' command and transfers this file via FTP to the ''dumpfiles'' directory of the hymfiles web directory.

== Dataset Export ==
Data sets that are intended to be automatically updated in the xBio:D IPT must be specified within the ''export_dwca_collections.py'' found within the ''cgi-bin'' of the web server. Exports are placed into the data exports directory of the web server and present for harvesting by a supplementary script found on the hymfiles server where the IPT resides.

== Automatic File Cleanup ==

The database server hosts the xBio:D database, the APIs, HOL, vSysLab, DB Manager, HNS, and the various HOL-based sites, however the available hard disk space is somewhat limited. Trace and log files quickly fill up available space that requires a solution that addresses the issue periodically. There are two scripts on server that remove temporary files that may cause problems.
* The first script, removeOldTraceFiles.py, removes the Oracle trace files used by the optimizer to make database usage efficient. If trace files are older than five days, the script will remove these files to save space.
* The second script, removeOldDataExports.py, removes data exports from the various web applications. This script removes any export that has resided on the server for over a month.
[[Category:OSUC Private]]

XBio:D Data Management

2015-09-18T16:10:12Z

Nfj:

----

'''xBio:D Data Management'''

This section provides instructions on performing common data management tasks on the xBio:D database that are not privy to general users. These tasks are not available through web applications and must either be performed by running a script or a database procedure.

== Change Occurrence (Specimen) Record CUID ==
In the Oracle SQL Developer, turn DBMS_OUTPUT on, then run the procedure <code>EXEC updateSpmID(old_cuid, new_cuid);</code>. The procedure will only produce output when a problem occurred.

== Remove Occurrence (Specimen) Record ==
In the Oracle SQL Developer, turn DBMS_OUTPUT on, then run the procedure <code>EXEC removeSpm(cuid);</code>. The procedure will only produce output when a problem occurred.

== Merged/Remove Locality Name ==
In the Oracle SQL Developer, turn DBMS_OUTPUT on, then run the procedure <code>EXEC change_locality(obsolete_loc_name, valid_loc_name);</code>. The procedure removes the obsolete locality and places all of the occurrence records from the obsolete locality into the valid locality name. There is also an additional, optional parameter ''coll_date'', which accepts the format DD-MON-YYYY, that will change the functioning of this procedure to change only those occurrence records that were collected on that particular date. If all of the occurrences were collected on that day, the locality is removed. The procedure will only produce output when a problem occurred.

== Add Collection Records or Taxon Checklist as a Project to the xBio:D IPT ==
# Log into the database server (''osuc.biosci.ohio-state.edu'') via SSH and open DwC-A collection export script, ''export_dwca_collections.py''. This script is set to run every Sunday at 8PM.
## <code>ssh [username]@osuc.biosci.ohio-state.edu</code>
## <code>sudo nano /var/www/cgi-bin/export_dwca_collections.py</code>
# Go to the ''handleDwCAExport'' function and add the taxon or collection you would like to export.
## The ''exportDwCA'' function of the OJ_Exporter package takes the collection ''Storage_Regime_ID'' as the identifier.
## The ''exportTaxonDwCA'' function of the OJ_Exporter package takes the taxon ''tnuid'' as the identifier.
# Execute the ''export_dwca_collections.py'' script immediately or wait until after the weekly export execution
# Download the DwC-A file created for the new collection or checklist
## Collection records example: ''http://osuc.biosci.ohio-state.edu/data_exports/dwca_1.zip''
## Taxon checklist example: ''http://osuc.biosci.ohio-state.edu/data_exports/dwca_tax_195000.zip''
# Create project in xBio:D IPT for the data you will be disseminating.
## Log into IPT at (''xbiod.osu.edu/ipt/'') and go to ''Manage Resources''
## Scroll to the bottom to ''Create New Resource'', specify a short name and resource type, then upload the previously exported file and create resource
## Fill in the metadata section of the resource with the appropriate values for provider, owner, etc.
# Log into the hymfiles server (''hymfiles.biosci.ohio-state.edu'') via Remote Desktop and open IPT DwC-A import script, ''populate_ipt.py''. The Python script is located in ''C:\backup_scripts''.
# Go to the ''handlePopulateIPT'' function and add the taxon or collection you would like to export.
## The numeric identifiers are the same as defined in the ''export'' step above
## The second parameter for the populate script is the resource short name specified above.
# Register and publish the new project. The resource will now be available on GBIF and can be shared with other data aggregators like iDigBio, VertNet, etc.

== Specialized Scripts for DB processing Tasks ==
These scripts include DOI lookup for xBio:D publication, processing the gender of people, and uploading of PDFs into Zenodo. The scripts are located in ''/scripts'' on the Database server.

== Aggregation Update ==
Many DB queries use tables that are aggregated from many separate tables to speed up processing. These aggregation tasks are performed automatically every Saturday under the DB job named ''aggregation_update''. These tasks include the following:
* '''''processDescriberIDs''''' - Goes through each taxonomic concept that does not already have a describer specified within the ''Protonym'' table and attempts to infer from an original description or replacement name literature annotation the author of the taxon. If a match is found, then the individual describer or describer party is added to the ''Protonym'' table.
* '''''update_people_stats''''' - Builds the ''AGGR_Person_Stats'' table that contains the # of occurrences collected, # of papers published, # of determinations made, # of distinct events collected, and the total # of contributions for each person.
* '''''update_genera_stats''''' - Builds the ''AGGR_Genus_Stats'' table that contains the # of occurrences determined, # of papers published, # of images taken, # of collections deposited, and distinct events collected for each tnuid.
* '''''update_place_children''''' - Builds the ''AGGR_Place_Children'' table that contains a place along with each subordinate place at any lower position within the geopolitical hierarchy.
* '''''update_taxon_children''''' - Builds the ''AGGR_Taxon_Children'' table that contains a tnuid along with each subordinate tnuid at any lower position within the taxonomic hierarchy. Species-group taxa are excluded as parent taxa within this table.
* '''''update_fossil_taxa''''' - Builds the ''AGGR_Fossil_Taxa'' table that contains a tcid for each taxon concept that is a fossil. Fossil status is only applied to species-group taxa, so this procedure also added taxa in which all of its subordinate taxa are fossils.
* '''''update_recordings''''' - Builds the ''AGGR_Taxon_Recordings'' table that contains a tnuid and recording info id for any recording that is contained within the taxon.
* '''''update_images''''' - Builds the ''AGGR_Taxon_Images'' table that contains a tnuid and image id for any specimen or taxon image that is contained within the taxon. Species-group taxa are excluded as parent taxa within this table.
* '''''update_habitats''''' - Builds the ''AGGR_Habitat'' table that contains a tnuid and habitat for any occurrence that is contained within the taxon. Species-group taxa are excluded as parent taxa within this table.
* '''''update_taxon_contributors''''' - Builds the ''AGGR_Taxon_Contribs'' table that contains a tnuid, contributor, and contribution flags for every contribution from the contributor within the taxon. Species-group taxa are excluded as parent taxa within this table.
* '''''update_inst_tcids''''' - Builds the ''AGGR_Inst_Tcids'' table that contains the tcids for every collection where an occurrence is present. Species-group taxa are excluded as parent taxa within this table.
* '''''update_associations''''' - Builds the ''AGGR_Taxon_Assocs'' table that contains a tnuid and associated tnuid for every taxon that is contained within the taxon. Species-group taxa are excluded as parent taxa within this table.

[[Category:OSUC Private]]

XBio:D Data Management

2015-09-18T15:51:20Z

Nfj:

----

'''xBio:D Data Management'''

This section provides instructions on performing common data management tasks on the xBio:D database that are not privy to general users. These tasks are not available through web applications and must either be performed by running a script or a database procedure.

== Change Occurrence (Specimen) Record CUID ==
In the Oracle SQL Developer, turn DBMS_OUTPUT on, then run the procedure <code>EXEC updateSpmID(old_cuid, new_cuid);</code>. The procedure will only produce output when a problem occurred.

== Remove Occurrence (Specimen) Record ==
In the Oracle SQL Developer, turn DBMS_OUTPUT on, then run the procedure <code>EXEC removeSpm(cuid);</code>. The procedure will only produce output when a problem occurred.

== Merged/Remove Locality Name ==
In the Oracle SQL Developer, turn DBMS_OUTPUT on, then run the procedure <code>EXEC change_locality(obsolete_loc_name, valid_loc_name);</code>. The procedure removes the obsolete locality and places all of the occurrence records from the obsolete locality into the valid locality name. There is also an additional, optional parameter ''coll_date'', which accepts the format DD-MON-YYYY, that will change the functioning of this procedure to change only those occurrence records that were collected on that particular date. If all of the occurrences were collected on that day, the locality is removed. The procedure will only produce output when a problem occurred.

== Add Collection Records or Taxon Checklist as a Project to the xBio:D IPT ==
# Log into the database server (''osuc.biosci.ohio-state.edu'') via SSH and open DwC-A collection export script, ''export_dwca_collections.py''. This script is set to run every Sunday at 8PM.
## <code>ssh [username]@osuc.biosci.ohio-state.edu</code>
## <code>sudo nano /var/www/cgi-bin/export_dwca_collections.py</code>
# Go to the ''handleDwCAExport'' function and add the taxon or collection you would like to export.
## The ''exportDwCA'' function of the OJ_Exporter package takes the collection ''Storage_Regime_ID'' as the identifier.
## The ''exportTaxonDwCA'' function of the OJ_Exporter package takes the taxon ''tnuid'' as the identifier.
# Execute the ''export_dwca_collections.py'' script immediately or wait until after the weekly export execution
# Download the DwC-A file created for the new collection or checklist
## Collection records example: ''http://osuc.biosci.ohio-state.edu/data_exports/dwca_1.zip''
## Taxon checklist example: ''http://osuc.biosci.ohio-state.edu/data_exports/dwca_tax_195000.zip''
# Create project in xBio:D IPT for the data you will be disseminating.
## Log into IPT at (''xbiod.osu.edu/ipt/'') and go to ''Manage Resources''
## Scroll to the bottom to ''Create New Resource'', specify a short name and resource type, then upload the previously exported file and create resource
## Fill in the metadata section of the resource with the appropriate values for provider, owner, etc.
# Log into the hymfiles server (''osuc.biosci.ohio-state.edu'') via Remote Desktop and open IPT DwC-A import script, ''populate_ipt.py''. The Python script is located in ''C:\backup_scripts''.
# Go to the ''handlePopulateIPT'' function and add the taxon or collection you would like to export.
## The numeric identifiers are the same as defined in the ''export'' step above
## The second parameter for the populate script is the resource short name specified above.
# Register and publish the new project. The resource will now be available on GBIF and can be shared with other data aggregators like iDigBio, VertNet, etc.

== Specialized Scripts for DB processing Tasks ==
These scripts include DOI lookup for xBio:D publication, processing the gender of people, and uploading of PDFs into Zenodo. The scripts are located in ''/scripts'' on the Database server.

== Aggregation Update ==
Many DB queries use tables that are aggregated from many separate tables to speed up processing. These aggregation tasks are performed automatically every Saturday under the DB job named ''aggregation_update''. These tasks include the following:
* '''''processDescriberIDs''''' - Goes through each taxonomic concept that does not already have a describer specified within the ''Protonym'' table and attempts to infer from an original description or replacement name literature annotation the author of the taxon. If a match is found, then the individual describer or describer party is added to the ''Protonym'' table.
* '''''update_people_stats''''' - Builds the ''AGGR_Person_Stats'' table that contains the # of occurrences collected, # of papers published, # of determinations made, # of distinct events collected, and the total # of contributions for each person.
* '''''update_genera_stats''''' - Builds the ''AGGR_Genus_Stats'' table that contains the # of occurrences determined, # of papers published, # of images taken, # of collections deposited, and distinct events collected for each tnuid.
* '''''update_place_children''''' - Builds the ''AGGR_Place_Children'' table that contains a place along with each subordinate place at any lower position within the geopolitical hierarchy.
* '''''update_taxon_children''''' - Builds the ''AGGR_Taxon_Children'' table that contains a tnuid along with each subordinate tnuid at any lower position within the taxonomic hierarchy. Species-group taxa are excluded as parent taxa within this table.
* '''''update_fossil_taxa''''' - Builds the ''AGGR_Fossil_Taxa'' table that contains a tcid for each taxon concept that is a fossil. Fossil status is only applied to species-group taxa, so this procedure also added taxa in which all of its subordinate taxa are fossils.
* '''''update_recordings''''' - Builds the ''AGGR_Taxon_Recordings'' table that contains a tnuid and recording info id for any recording that is contained within the taxon.
* '''''update_images''''' - Builds the ''AGGR_Taxon_Images'' table that contains a tnuid and image id for any specimen or taxon image that is contained within the taxon. Species-group taxa are excluded as parent taxa within this table.
* '''''update_habitats''''' - Builds the ''AGGR_Habitat'' table that contains a tnuid and habitat for any occurrence that is contained within the taxon. Species-group taxa are excluded as parent taxa within this table.
* '''''update_taxon_contributors''''' - Builds the ''AGGR_Taxon_Contribs'' table that contains a tnuid, contributor, and contribution flags for every contribution from the contributor within the taxon. Species-group taxa are excluded as parent taxa within this table.
* '''''update_inst_tcids''''' - Builds the ''AGGR_Inst_Tcids'' table that contains the tcids for every collection where an occurrence is present. Species-group taxa are excluded as parent taxa within this table.
* '''''update_associations''''' - Builds the ''AGGR_Taxon_Assocs'' table that contains a tnuid and associated tnuid for every taxon that is contained within the taxon. Species-group taxa are excluded as parent taxa within this table.

[[Category:OSUC Private]]