documentation:input:taxonomy
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documentation:input:taxonomy [2013/07/17 11:23] kmartinez_nhm [Entering new taxa from scratch] |
documentation:input:taxonomy [2014/03/18 13:00] (current) armin_loeckher |
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| **__Recommendation:__** \\ \\ | **__Recommendation:__** \\ \\ | ||
| - | === Adding annotations in new herbarium labels === | + | === Adding annotation labels === |
| - | If your specimen is the type for a later synonymised name, and the accepted name does not appear in the herbarium sheet, you will need to add an annotation on a herbarium label. Here you should include: (1) the information source (e.g. "fide TROPICOS" or "fide R. Govaerts & al. 2008. World checklist of Myrtaceae"); (2) the accepted name (e.g. ≡ //Picea abies// or = //Picea abies//, depending on whether the names are homotypic or heterotypic synonyms, respectively); and (3) the name and affiliation of the reviser, and the revision date (e. g. "annot. P. Escobar García (W) 2013-06"). \\ | + | If your specimen is the type for a later synonymized name, and the accepted name does not appear on the herbarium sheet, you will need to add an annotation label. Here you should include: (1) the information source (e.g. "fide TROPICOS" or "fide R. Govaerts & al. 2008. World checklist of Myrtaceae"); (2) the accepted name (e.g. ≡ //Picea abies// or = //Picea abies//, depending on whether the names are homotypic or heterotypic synonyms, respectively); and (3) the name and affiliation of the reviser, and the revision date (e. g. "annot. P. Escobar García (W) 2013-06"). \\ |
| - | > Note: Only add a new herbarium label for information that is completely different to that given on herbarium sheet such as: type status, basionym, accepted name, author(s). If there is only a slight divergence i.e. a missing "ex …" in the authorship there is no need for a new label). | + | > Note: Only add an annotation label for information that is completely different to that given on the herbarium sheet such as: type status, basionym, accepted name, author(s). If there is only a slight divergence i.e. a missing "ex …" in the authorship there is no need for a new label). |
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| First, enter the //Pinus abies// L. **edit Species** form by searching in **list Species** or as already explained in the previous section. \\ | First, enter the //Pinus abies// L. **edit Species** form by searching in **list Species** or as already explained in the previous section. \\ | ||
| - | {{ https://docs.google.com/drawings/d/1H5psrRWfh5X8ZSwYXm6i_ruIAR6FrxRcFP7O8g_8KzM/pub?w=904&h=714&.png?904x714 }} | + | {{ https://docs.google.com/drawings/d/1H5psrRWfh5X8ZSwYXm6i_ruIAR6FrxRcFP7O8g_8KzM/pub?w=904&h=714&.png?904x714 | nomenclature 27}} |
| Then click **New & Copy** at the bottom of the **edit Species** form. Edit the required fields, in our case **Author** and **accepted Taxon**. \\ | Then click **New & Copy** at the bottom of the **edit Species** form. Edit the required fields, in our case **Author** and **accepted Taxon**. \\ | ||
| - | {{ https://docs.google.com/drawings/d/1aDjGC_E9JlrJeK3kq2xt3m-LvI4badIW5TqEq82JcUk/pub?w=960&h=720&.png?960x720 }} | + | {{ https://docs.google.com/drawings/d/1aDjGC_E9JlrJeK3kq2xt3m-LvI4badIW5TqEq82JcUk/pub?w=960&h=720&.png?960x720 | nomenclature 28}} |
| Click **Insert**. \\ | Click **Insert**. \\ | ||
| Line 182: | Line 182: | ||
| Start by selecting **Taxonomy** in the main menu and then clicking **new entry** in the **list Species** form. \\ | Start by selecting **Taxonomy** in the main menu and then clicking **new entry** in the **list Species** form. \\ | ||
| - | {{ https://docs.google.com/drawings/d/10jbaWNwISdzyg0l6Y4h_HOtvh0vO-Q31snNpSYGY6Mw/pub?w=970&h=336&.png?970x336 }} | + | {{ https://docs.google.com/drawings/d/10jbaWNwISdzyg0l6Y4h_HOtvh0vO-Q31snNpSYGY6Mw/pub?w=970&h=336&.png?970x336 | nomenclature 29}} |
| This opens a new **edit Species** form. \\ | This opens a new **edit Species** form. \\ | ||
| - | {{ https://docs.google.com/drawings/d/14JDZJQjwkQXxvky7ruKYuqz9YB-Xa4ype_a5c0GxSVw/pub?w=924&h=714&.png?924x714 }} | + | {{ https://docs.google.com/drawings/d/14JDZJQjwkQXxvky7ruKYuqz9YB-Xa4ype_a5c0GxSVw/pub?w=924&h=714&.png?924x714 | nomenclature 30}} |
| Make sure that the genus is not yet entered in the database, paying special attention to the existence of possible orthographic variants. Write the new genus (e. g. //Razafimandimbisonia//) in the **Genus** field and a drop-down list will display the genera already present in the database with their corresponding authors, families and identity numbers. Please note the possible existence of homonymous genera in the database. Always ay attention the author and family! \\ | Make sure that the genus is not yet entered in the database, paying special attention to the existence of possible orthographic variants. Write the new genus (e. g. //Razafimandimbisonia//) in the **Genus** field and a drop-down list will display the genera already present in the database with their corresponding authors, families and identity numbers. Please note the possible existence of homonymous genera in the database. Always ay attention the author and family! \\ | ||
| Line 192: | Line 192: | ||
| In our example //Razafimandimbisonia// is not yet entered in the database. \\ | In our example //Razafimandimbisonia// is not yet entered in the database. \\ | ||
| - | {{ https://docs.google.com/drawings/d/1Vg6CBndaVzL9lSD5a9vyFTz3REoY3Mom11BCPgYAl9A/pub?w=800&h=710&.png?800x710 }} | + | {{ https://docs.google.com/drawings/d/1Vg6CBndaVzL9lSD5a9vyFTz3REoY3Mom11BCPgYAl9A/pub?w=800&h=710&.png?800x710 | nomenclature 31}} |
| Open the **edit Genera** window by clicking **Genus** in the new **edit Species** window. \\ | Open the **edit Genera** window by clicking **Genus** in the new **edit Species** window. \\ | ||
| - | {{ https://docs.google.com/drawings/d/1q6hQEMeCw8Vr6X4Eib8Y8ztO-jce2HIUxWfhAeEhhwo/pub?w=763&h=719&.png?763x719 }} | + | {{ https://docs.google.com/drawings/d/1q6hQEMeCw8Vr6X4Eib8Y8ztO-jce2HIUxWfhAeEhhwo/pub?w=763&h=719&.png?763x719 | nomenclature 32}} |
| Start by entering //Razafimandimbisonia// in the **Genus** field (there is no drop-down list here), then the author in the **Author** field. Choose family using the **Family** field. Check always for the genus name in Index Nominum Genericorum [[http://botany.si.edu/ing/|ING]]. If the genus you want to enter is not there this should be noted in the **Remarks** field. Add a type species if known. | Start by entering //Razafimandimbisonia// in the **Genus** field (there is no drop-down list here), then the author in the **Author** field. Choose family using the **Family** field. Check always for the genus name in Index Nominum Genericorum [[http://botany.si.edu/ing/|ING]]. If the genus you want to enter is not there this should be noted in the **Remarks** field. Add a type species if known. | ||
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| Click **Insert** when you are ready, making sure that everything is correct as the fields will no longer be editable after. The **edit Genera** window will close. \\ | Click **Insert** when you are ready, making sure that everything is correct as the fields will no longer be editable after. The **edit Genera** window will close. \\ | ||
| - | {{ https://docs.google.com/drawings/d/1BzVFvUsVNdGPBFIFUGVDB4p-r2VIDJqksUusYaaAY1o/pub?w=782&h=722&.png?782x722 }} | + | {{ https://docs.google.com/drawings/d/1BzVFvUsVNdGPBFIFUGVDB4p-r2VIDJqksUusYaaAY1o/pub?w=782&h=722&.png?782x722 | nomenclature 33}} |
| Now back in the **edit Species** form enter the author(s) in the **Author** field and choose genus in Rank. Then press the **Insert** button. \\ | Now back in the **edit Species** form enter the author(s) in the **Author** field and choose genus in Rank. Then press the **Insert** button. \\ | ||
| - | {{ https://docs.google.com/drawings/d/15UWO-2P9X0ActwNlnI-o0IUMzNyS1yFMJat2X18TEJ0/pub?w=787&h=723&.png?787x723 }} | + | {{ https://docs.google.com/drawings/d/15UWO-2P9X0ActwNlnI-o0IUMzNyS1yFMJat2X18TEJ0/pub?w=787&h=723&.png?787x723 | nomenclature 34}} |
| ---- | ---- | ||
| Line 218: | Line 218: | ||
| Open a new **edit Species** form, enter the genus name (for example //Potamogeton//) and choose **Genus** in the **Rank** field. Then choose **x** in the **tax. Status** field. Then click **Insert**. This makes the field **tax. Status** change into **parents**. By clicking on the **parents** button, you can enter the parental species. Save changes by clicking **Insert** when finished. The hybrid formula will appear on top line of the **edit Species** page, besides the taxonID and change the **Rank** field to **species**. \\ | Open a new **edit Species** form, enter the genus name (for example //Potamogeton//) and choose **Genus** in the **Rank** field. Then choose **x** in the **tax. Status** field. Then click **Insert**. This makes the field **tax. Status** change into **parents**. By clicking on the **parents** button, you can enter the parental species. Save changes by clicking **Insert** when finished. The hybrid formula will appear on top line of the **edit Species** page, besides the taxonID and change the **Rank** field to **species**. \\ | ||
| - | {{ https://docs.google.com/drawings/d/1mKnebC_PfsEVNxTf_YjH_ksUzJF9GBp0ZxBWXNywt6Y/pub?w=856&h=675&.png?856x675 | nomenclature 35}} | + | {{ https://docs.google.com/drawings/d/1mKnebC_PfsEVNxTf_YjH_ksUzJF9GBp0ZxBWXNywt6Y/pub?w=856&h=675&.png?856x675 | nomenclature 35 "Because **** you thats why":oP }} |
| Hybrid formulas appear only as a genus name in the drop-down lists of the **accepted Taxon** or **Basionym** fields (each with its own ID number). To search for hybrid formulas go to the **list Species** form, input the relevant genus name and select **x** in **Status**. \\ | Hybrid formulas appear only as a genus name in the drop-down lists of the **accepted Taxon** or **Basionym** fields (each with its own ID number). To search for hybrid formulas go to the **list Species** form, input the relevant genus name and select **x** in **Status**. \\ | ||
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| Information regarding types and typification should be entered in the database at two levels: **Specimens** and **Taxonomy**. In the **edit Specimens** form the **T** field allows you to choose the kind of type from a drop-down list (holo-, isolecto-, syn-, etc.). The field **typified by** should be filled in with the information available on the researcher who typified the voucher. Enter the researcher´s name, their herbarium or institutional acronym in brackets [e.g. (M) for Munich] and the date of the typification [e.g. S. Zarre (M) 1994]. \\ | Information regarding types and typification should be entered in the database at two levels: **Specimens** and **Taxonomy**. In the **edit Specimens** form the **T** field allows you to choose the kind of type from a drop-down list (holo-, isolecto-, syn-, etc.). The field **typified by** should be filled in with the information available on the researcher who typified the voucher. Enter the researcher´s name, their herbarium or institutional acronym in brackets [e.g. (M) for Munich] and the date of the typification [e.g. S. Zarre (M) 1994]. \\ | ||
| - | {{ https://docs.google.com/drawings/d/1tnFDzmYLqAJg4Jb0A27ijqYl6AusdJc9_uP8qqQg1s8/pub?w=735&h=719&.png?735x719 }} | + | {{ https://docs.google.com/drawings/d/1tnFDzmYLqAJg4Jb0A27ijqYl6AusdJc9_uP8qqQg1s8/pub?w=735&h=719&.png?735x719 | nomenclature 37}} |
| Clicking on **T** opens the **list Specimens Types** window. Here, you should enter the names a given specimen is the type for. Click **add new line** to start inputting information and a second window **edit Specimens Types** will open. Enter the basionym in **taxon** (here only basionyms are correct), the kind of type in **type**, the reviser with institution acronym in **typified by** and date if available in **date**. Any further information can be added in **annotations** [e. g. information about lectotypification (please add the reference), divergent opinions about the typifications, etc.]. Click **Insert** to save and close the **list Specimens Types** window. \\ | Clicking on **T** opens the **list Specimens Types** window. Here, you should enter the names a given specimen is the type for. Click **add new line** to start inputting information and a second window **edit Specimens Types** will open. Enter the basionym in **taxon** (here only basionyms are correct), the kind of type in **type**, the reviser with institution acronym in **typified by** and date if available in **date**. Any further information can be added in **annotations** [e. g. information about lectotypification (please add the reference), divergent opinions about the typifications, etc.]. Click **Insert** to save and close the **list Specimens Types** window. \\ | ||
| - | {{ https://docs.google.com/drawings/d/1SVs82k9rwEwiW2fIcN-xEvQHXBvXWGNwMzL347x2HbM/pub?w=959&h=561&.png?959x561 }} | + | {{ https://docs.google.com/drawings/d/1SVs82k9rwEwiW2fIcN-xEvQHXBvXWGNwMzL347x2HbM/pub?w=959&h=561&.png?959x561 | nomenclature 38}} |
| Note that a given specimen can be the type of more than one name, or that different revisers may hold conflicting or complementary opinions. In this case, use **add new line** to enter further typifications as explained before. If a certain species is type for a genus, you need to add this information to the type specimen. \\ | Note that a given specimen can be the type of more than one name, or that different revisers may hold conflicting or complementary opinions. In this case, use **add new line** to enter further typifications as explained before. If a certain species is type for a genus, you need to add this information to the type specimen. \\ | ||
| - | {{ https://docs.google.com/drawings/d/1lZP26cha3mMqhQTxD4aPrsz6lgku7VGIFZX6tmaBKH4/pub?w=955&h=317&.png?955x317 }} | + | {{ https://docs.google.com/drawings/d/1lZP26cha3mMqhQTxD4aPrsz6lgku7VGIFZX6tmaBKH4/pub?w=955&h=317&.png?955x317 | nomenclature 39}} |
| Above the **Genus** field there is the **type specimens** button, which allows you to check the typification entries for the relevant taxon. This opens the **list Specimens** window, which displays the typified name (basionym) on the top with all the entered specimens listed under their accepted names. The **specimens** button takes you to the main **list Specimens** window where you will see all the specimens entered under the name, including those that are not types for that name. The number in brackets next to each button indicates the number of entries in each case.\\ | Above the **Genus** field there is the **type specimens** button, which allows you to check the typification entries for the relevant taxon. This opens the **list Specimens** window, which displays the typified name (basionym) on the top with all the entered specimens listed under their accepted names. The **specimens** button takes you to the main **list Specimens** window where you will see all the specimens entered under the name, including those that are not types for that name. The number in brackets next to each button indicates the number of entries in each case.\\ | ||
| - | {{ https://docs.google.com/drawings/d/1vanQeZs59TeF2ufNqWKPNm6t5J2A-DpAdDR1pghoBXs/pub?w=960&h=720&.png?960x720 }} | + | {{ https://docs.google.com/drawings/d/1vanQeZs59TeF2ufNqWKPNm6t5J2A-DpAdDR1pghoBXs/pub?w=960&h=720&.png?960x720 | nomenclature 40}} |
| ---- | ---- | ||
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| === Taxonomy === | === Taxonomy === | ||
| + | * [[http://www.anbg.gov.au/cgi-bin/apni|APNI]]: The Australian Plant Name Index of Australian Plant Census (CHAH). | ||
| + | * [[http://ww2.bgbm.org/EuroPlusMed/query.asp|Euro+Med]]: Taxonomic and floristic information from the Flora Europaea and Med-Checklist areas. | ||
| + | * [[http://http://www.ildis.org/|ILDIS]]: The International Legume Database & Information Service. | ||
| + | * [[http://botany.si.edu/ing/|ING]]: The Index Nominum Genericorum, a compilation of generic names published for organisms. | ||
| + | * [[http://www.ipni.org/ipni/plantnamesearchpage.do|IPNI]]: The International Plant Names Index, a database of names and associated basic bibliographical details. | ||
| * [[http://www.theplantlist.org/|The Plant List]]: Kew’s working list of all known vascular plants. | * [[http://www.theplantlist.org/|The Plant List]]: Kew’s working list of all known vascular plants. | ||
| + | * [[http://http://compositae.landcareresearch.co.nz/|TICA]]: The Global Compositae Checklist. | ||
| * [[http://www.tropicos.org/|TROPICOS]]: Missouri Botanical Garden’s database of nomenclature, bibliography and specimens. | * [[http://www.tropicos.org/|TROPICOS]]: Missouri Botanical Garden’s database of nomenclature, bibliography and specimens. | ||
| - | * [[http://www.ipni.org/ipni/plantnamesearchpage.do|IPNI]]: The International Plant Names Index, a database of names and associated basic bibliographical details. | ||
| * [[http://apps.kew.org/wcsp/home.do|WCSP]]: The World Checklist of Selected Plant Families. | * [[http://apps.kew.org/wcsp/home.do|WCSP]]: The World Checklist of Selected Plant Families. | ||
| - | * [[http://ww2.bgbm.org/EuroPlusMed/query.asp|Euro+Med]]: Taxonomic and floristic information from the Flora Europaea and Med-Checklist areas. | ||
| - | * [[http://http://compositae.landcareresearch.co.nz/|TICA]]: The Global Compositae Checklist. | ||
| - | * [[http://http://www.ildis.org/|ILDIS]]: The International Legume Database & Information Service. | ||
| - | * [[http://botany.si.edu/ing/|ING]]: The Index Nominum Genericorum, a compilation of generic names published for organisms. | ||
| - | * [[http://www.anbg.gov.au/cgi-bin/apni|APNI]]: The Australian Plant Name Index of Australian Plant Census (CHAH). | ||
| === Literature online === | === Literature online === | ||
| + | * [[http://www.biodiversitylibrary.org/|BHL]]: The Biodiversity Heritage Library. | ||
| + | * [[http://bibdigital.rjb.csic.es/ing/index.php|Biblioteca digital]]: The digital library of the Madrid Botanical Garden. | ||
| * [[http://gallica.bnf.fr/?lang=DE|GALLICA]]: The digital library of the Bibliothèque Nationale de France. | * [[http://gallica.bnf.fr/?lang=DE|GALLICA]]: The digital library of the Bibliothèque Nationale de France. | ||
| + | * [[http://archive.org/details/texts|Internet Archive]]: A non-profit organisation providing a vast permanant digital library. | ||
| * [[http://www.digitale-sammlungen.de/|MDZ]]: The digital library of the Bavarian State Library. | * [[http://www.digitale-sammlungen.de/|MDZ]]: The digital library of the Bavarian State Library. | ||
| - | * [[http://www.biodiversitylibrary.org/|BHL]]: The Biodiversity Heritage Library. | ||
| - | * [[http://bibdigital.rjb.csic.es/ing/index.php|Biblioteca digital]]: The digital library of the Madrid Botanical Garden. | ||
| === Further useful links === | === Further useful links === | ||
| Line 279: | Line 280: | ||
| * [[http://www.iapt-taxon.org/icbn/main.htm| The Appendix III (NOMINA GENERICA CONSERVANDA ET REJICIENDA) of Vienna Code]]. | * [[http://www.iapt-taxon.org/icbn/main.htm| The Appendix III (NOMINA GENERICA CONSERVANDA ET REJICIENDA) of Vienna Code]]. | ||
| - | Pedro's diagram (Google docs) [[https://docs.google.com/drawings/d/1e3ps2m_nZvAe0oa9B_q1ydXrm60WyNJnasCQm7XwnX4/edit|type categories]]. \\ | + | Pedro's diagram (Google docs) [[https://docs.google.com/drawings/d/1e3ps2m_nZvAe0oa9B_q1ydXrm60WyNJnasCQm7XwnX4/edit?usp=sharing|type categories]]. \\ |
| - | Karen´s diagram (Google docs)[[https://docs.google.com/drawings/d/1oWqASw_DmBt3zcUisGl2gPVRhErh1l_WzAeJ4_nkH1s/edit|specimen typification]]. \\ | + | Karen´s diagram (Google docs)[[https://docs.google.com/drawings/d/1oWqASw_DmBt3zcUisGl2gPVRhErh1l_WzAeJ4_nkH1s/edit?usp=sharing|specimen typification]]. \\ |
| - | Name categories diagram (Google docs) [[https://docs.google.com/drawings/d/10VtnxORj0ALVmSeHMnXPsJYS2abbSCPf2i8a4vkesRQ/edit|Name categories diagram]]. \\ | + | Name categories diagram (Google docs) [[https://docs.google.com/drawings/d/10VtnxORj0ALVmSeHMnXPsJYS2abbSCPf2i8a4vkesRQ/edit?usp=sharing|Name categories diagram]]. \\ |
| - | Captures of name categories diagram (Google docs) [[https://docs.google.com/document/d/1lvuavOx3jp_3oux9wQeKNtHFAPxAuaYejUD3kfCHfxg/edit|Captures of name categories diagram]]. \\ \\ | + | Captures of name categories diagram (Google docs) [[https://docs.google.com/document/d/1lvuavOx3jp_3oux9wQeKNtHFAPxAuaYejUD3kfCHfxg/edit?usp=sharing|Captures of name categories diagram]]. \\ \\ |
| Line 292: | Line 293: | ||
| __**Case 1**__ \\ | __**Case 1**__ \\ | ||
| - | Dealing with a lectotypified taxon consisting of several syntypes which are recently linked to different accepted taxa you might have problems to print labels from those syntypes not linked to the lectotype. The accepted taxon on the printed labels will always be that of the lectotypified specimen independent of the syntypes. \\ | + | Dealing with a lectotypified taxon consisting of several syntypes which are recently linked to different accepted taxa, you may have problems to print labels for the syntypes. The accepted taxon on the printed labels will always be that of the lectotypified specimen independent of the syntypes. \\ |
| - | In such a case you have to change temporarily the accepted taxon on the **edit species** page in **accepted taxon** to be correctly linked to that syntype which you need and is not the lectotype. After safing your changes you can print the labels. | + | In such a case you have to temporarily change the accepted taxon on the **edit species** page in **accepted taxon** to the name which you need to appear on the label. After saving your changes, you can print the labels. |
| - | It is very important not to forget to change back again the name of the accepted taxon to that one of the lectotypified syntype. | + | Remember to change the accepted taxon back to that of the lectotypified syntype. |
| ### mit Beispiel und vermutlich auch screenshots ###### | ### mit Beispiel und vermutlich auch screenshots ###### | ||
documentation/input/taxonomy.1374060206.txt.gz · Last modified: 2013/07/17 11:23 by kmartinez_nhm
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